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32,200 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/HelixAxisAligner.java | HelixAxisAligner.getMidPoint | private Point3d getMidPoint(Point3d p1, Point3d p2, Point3d p3) {
Vector3d v1 = new Vector3d();
v1.sub(p1, p2);
Vector3d v2 = new Vector3d();
v2.sub(p3, p2);
Vector3d v3 = new Vector3d();
v3.add(v1);
v3.add(v2);
v3.normalize();
// calculat the total distance between to subunits
double dTotal = v1.length();
// calculate the rise along the y-axis. The helix axis is aligned with y-axis,
// therfore, the rise between subunits is the y-distance
double rise = p2.y - p1.y;
// use phythagorean theoremm to calculate chord length between two subunit centers
double chord = Math.sqrt(dTotal*dTotal - rise*rise);
// System.out.println("Chord d: " + dTotal + " rise: " + rise + "chord: " + chord);
double angle = helixLayers.getByLargestContacts().getAxisAngle().angle;
// using the axis angle and the chord length, we can calculate the radius of the helix
// http://en.wikipedia.org/wiki/Chord_%28geometry%29
double radius = chord/Math.sin(angle/2)/2; // can this go to zero?
// System.out.println("Radius: " + radius);
// project the radius onto the vector that points toward the helix axis
v3.scale(radius);
v3.add(p2);
// System.out.println("Angle: " + Math.toDegrees(helixLayers.getByLowestAngle().getAxisAngle().angle));
Point3d cor = new Point3d(v3);
return cor;
} | java | private Point3d getMidPoint(Point3d p1, Point3d p2, Point3d p3) {
Vector3d v1 = new Vector3d();
v1.sub(p1, p2);
Vector3d v2 = new Vector3d();
v2.sub(p3, p2);
Vector3d v3 = new Vector3d();
v3.add(v1);
v3.add(v2);
v3.normalize();
// calculat the total distance between to subunits
double dTotal = v1.length();
// calculate the rise along the y-axis. The helix axis is aligned with y-axis,
// therfore, the rise between subunits is the y-distance
double rise = p2.y - p1.y;
// use phythagorean theoremm to calculate chord length between two subunit centers
double chord = Math.sqrt(dTotal*dTotal - rise*rise);
// System.out.println("Chord d: " + dTotal + " rise: " + rise + "chord: " + chord);
double angle = helixLayers.getByLargestContacts().getAxisAngle().angle;
// using the axis angle and the chord length, we can calculate the radius of the helix
// http://en.wikipedia.org/wiki/Chord_%28geometry%29
double radius = chord/Math.sin(angle/2)/2; // can this go to zero?
// System.out.println("Radius: " + radius);
// project the radius onto the vector that points toward the helix axis
v3.scale(radius);
v3.add(p2);
// System.out.println("Angle: " + Math.toDegrees(helixLayers.getByLowestAngle().getAxisAngle().angle));
Point3d cor = new Point3d(v3);
return cor;
} | [
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of three adjacent subunit centers.
@param p1 center of first subunit
@param p2 center of second subunit
@param p3 center of third subunit
@return midpoint of helix | [
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32,201 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/HelixAxisAligner.java | HelixAxisAligner.calcBoundaries | private void calcBoundaries() {
minBoundary.x = Double.MAX_VALUE;
maxBoundary.x = Double.MIN_VALUE;
minBoundary.y = Double.MAX_VALUE;
maxBoundary.x = Double.MIN_VALUE;
minBoundary.z = Double.MAX_VALUE;
maxBoundary.z = Double.MIN_VALUE;
xzRadiusMax = Double.MIN_VALUE;
Point3d probe = new Point3d();
for (Point3d[] list: subunits.getTraces()) {
for (Point3d p: list) {
probe.set(p);
transformationMatrix.transform(probe);
minBoundary.x = Math.min(minBoundary.x, probe.x);
maxBoundary.x = Math.max(maxBoundary.x, probe.x);
minBoundary.y = Math.min(minBoundary.y, probe.y);
maxBoundary.y = Math.max(maxBoundary.y, probe.y);
minBoundary.z = Math.min(minBoundary.z, probe.z);
maxBoundary.z = Math.max(maxBoundary.z, probe.z);
xzRadiusMax = Math.max(xzRadiusMax, Math.sqrt(probe.x*probe.x + probe.z * probe.z));
}
}
// System.out.println("MinBoundary: " + minBoundary);
// System.out.println("MaxBoundary: " + maxBoundary);
// System.out.println("zxRadius: " + xzRadiusMax);
} | java | private void calcBoundaries() {
minBoundary.x = Double.MAX_VALUE;
maxBoundary.x = Double.MIN_VALUE;
minBoundary.y = Double.MAX_VALUE;
maxBoundary.x = Double.MIN_VALUE;
minBoundary.z = Double.MAX_VALUE;
maxBoundary.z = Double.MIN_VALUE;
xzRadiusMax = Double.MIN_VALUE;
Point3d probe = new Point3d();
for (Point3d[] list: subunits.getTraces()) {
for (Point3d p: list) {
probe.set(p);
transformationMatrix.transform(probe);
minBoundary.x = Math.min(minBoundary.x, probe.x);
maxBoundary.x = Math.max(maxBoundary.x, probe.x);
minBoundary.y = Math.min(minBoundary.y, probe.y);
maxBoundary.y = Math.max(maxBoundary.y, probe.y);
minBoundary.z = Math.min(minBoundary.z, probe.z);
maxBoundary.z = Math.max(maxBoundary.z, probe.z);
xzRadiusMax = Math.max(xzRadiusMax, Math.sqrt(probe.x*probe.x + probe.z * probe.z));
}
}
// System.out.println("MinBoundary: " + minBoundary);
// System.out.println("MaxBoundary: " + maxBoundary);
// System.out.println("zxRadius: " + xzRadiusMax);
} | [
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32,202 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java | MultipleAlignmentJmol.getJmolString | public static String getJmolString(MultipleAlignment multAln,
List<Atom[]> transformedAtoms, ColorBrewer colorPalette,
boolean colorByBlocks) {
// Color by blocks if specified
if (colorByBlocks)
return getMultiBlockJmolString(multAln, transformedAtoms,
colorPalette, colorByBlocks);
Color[] colors = colorPalette.getColorPalette(multAln.size());
StringBuffer j = new StringBuffer();
j.append(DEFAULT_SCRIPT);
// Color the equivalent residues of every structure
StringBuffer sel = new StringBuffer();
sel.append("select *; color lightgrey; backbone 0.1; ");
List<List<String>> allPDB = new ArrayList<List<String>>();
// Get the aligned residues of every structure
for (int i = 0; i < multAln.size(); i++) {
List<String> pdb = MultipleAlignmentJmolDisplay.getPDBresnum(i,
multAln, transformedAtoms.get(i));
allPDB.add(pdb);
sel.append("select ");
int pos = 0;
for (String res : pdb) {
if (pos > 0)
sel.append(",");
pos++;
sel.append(res);
sel.append("/" + (i + 1));
}
if (pos == 0)
sel.append("none");
sel.append("; backbone 0.3 ; color [" + colors[i].getRed() + ","
+ colors[i].getGreen() + "," + colors[i].getBlue() + "]; ");
}
j.append(sel);
j.append("model 0; ");
j.append(LIGAND_DISPLAY_SCRIPT);
return j.toString();
} | java | public static String getJmolString(MultipleAlignment multAln,
List<Atom[]> transformedAtoms, ColorBrewer colorPalette,
boolean colorByBlocks) {
// Color by blocks if specified
if (colorByBlocks)
return getMultiBlockJmolString(multAln, transformedAtoms,
colorPalette, colorByBlocks);
Color[] colors = colorPalette.getColorPalette(multAln.size());
StringBuffer j = new StringBuffer();
j.append(DEFAULT_SCRIPT);
// Color the equivalent residues of every structure
StringBuffer sel = new StringBuffer();
sel.append("select *; color lightgrey; backbone 0.1; ");
List<List<String>> allPDB = new ArrayList<List<String>>();
// Get the aligned residues of every structure
for (int i = 0; i < multAln.size(); i++) {
List<String> pdb = MultipleAlignmentJmolDisplay.getPDBresnum(i,
multAln, transformedAtoms.get(i));
allPDB.add(pdb);
sel.append("select ");
int pos = 0;
for (String res : pdb) {
if (pos > 0)
sel.append(",");
pos++;
sel.append(res);
sel.append("/" + (i + 1));
}
if (pos == 0)
sel.append("none");
sel.append("; backbone 0.3 ; color [" + colors[i].getRed() + ","
+ colors[i].getGreen() + "," + colors[i].getBlue() + "]; ");
}
j.append(sel);
j.append("model 0; ");
j.append(LIGAND_DISPLAY_SCRIPT);
return j.toString();
} | [
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32,203 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java | MultipleAlignmentJmol.getMultiBlockJmolString | public static String getMultiBlockJmolString(MultipleAlignment multAln,
List<Atom[]> transformedAtoms, ColorBrewer colorPalette,
boolean colorByBlocks) {
StringWriter jmol = new StringWriter();
jmol.append(DEFAULT_SCRIPT);
jmol.append("select *; color lightgrey; backbone 0.1; ");
int blockNum = multAln.getBlocks().size();
Color[] colors = colorPalette.getColorPalette(blockNum);
// For every structure color all the blocks with the printBlock method
for (int str = 0; str < transformedAtoms.size(); str++) {
jmol.append("select */" + (str + 1) + "; color lightgrey; model "
+ (str + 1) + "; ");
int index = 0;
for (BlockSet bs : multAln.getBlockSets()) {
for (Block b : bs.getBlocks()) {
List<List<Integer>> alignRes = b.getAlignRes();
printJmolScript4Block(transformedAtoms.get(str), alignRes,
colors[index], jmol, str, index, blockNum);
index++;
}
}
}
jmol.append("model 0; ");
jmol.append(LIGAND_DISPLAY_SCRIPT);
return jmol.toString();
} | java | public static String getMultiBlockJmolString(MultipleAlignment multAln,
List<Atom[]> transformedAtoms, ColorBrewer colorPalette,
boolean colorByBlocks) {
StringWriter jmol = new StringWriter();
jmol.append(DEFAULT_SCRIPT);
jmol.append("select *; color lightgrey; backbone 0.1; ");
int blockNum = multAln.getBlocks().size();
Color[] colors = colorPalette.getColorPalette(blockNum);
// For every structure color all the blocks with the printBlock method
for (int str = 0; str < transformedAtoms.size(); str++) {
jmol.append("select */" + (str + 1) + "; color lightgrey; model "
+ (str + 1) + "; ");
int index = 0;
for (BlockSet bs : multAln.getBlockSets()) {
for (Block b : bs.getBlocks()) {
List<List<Integer>> alignRes = b.getAlignRes();
printJmolScript4Block(transformedAtoms.get(str), alignRes,
colors[index], jmol, str, index, blockNum);
index++;
}
}
}
jmol.append("model 0; ");
jmol.append(LIGAND_DISPLAY_SCRIPT);
return jmol.toString();
} | [
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32,204 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GridCell.java | GridCell.getContactsWithinCell | public List<Contact> getContactsWithinCell(){
List<Contact> contacts = new ArrayList<Contact>();
Point3d[] iAtoms = grid.getIAtoms();
Point3d[] jAtoms = grid.getJAtoms();
double cutoff = grid.getCutoff();
if (jAtoms==null) {
for (int i:iIndices) {
for (int j:iIndices) {
if (j>i) {
double distance = iAtoms[i].distance(iAtoms[j]);
if (distance<cutoff) contacts.add(new Contact(i, j, distance));
}
}
}
} else {
for (int i:iIndices) {
for (int j:jIndices) {
double distance = iAtoms[i].distance(jAtoms[j]);
if (distance<cutoff) contacts.add(new Contact(i, j, distance));
}
}
}
return contacts;
} | java | public List<Contact> getContactsWithinCell(){
List<Contact> contacts = new ArrayList<Contact>();
Point3d[] iAtoms = grid.getIAtoms();
Point3d[] jAtoms = grid.getJAtoms();
double cutoff = grid.getCutoff();
if (jAtoms==null) {
for (int i:iIndices) {
for (int j:iIndices) {
if (j>i) {
double distance = iAtoms[i].distance(iAtoms[j]);
if (distance<cutoff) contacts.add(new Contact(i, j, distance));
}
}
}
} else {
for (int i:iIndices) {
for (int j:jIndices) {
double distance = iAtoms[i].distance(jAtoms[j]);
if (distance<cutoff) contacts.add(new Contact(i, j, distance));
}
}
}
return contacts;
} | [
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If {@link Grid#getJAtoms()} is null, distances are within the iAtoms only
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32,205 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GridCell.java | GridCell.hasContactToAtom | public boolean hasContactToAtom(Point3d[] iAtoms, Point3d[] jAtoms, Point3d query, double cutoff) {
for( int i : iIndices ) {
double distance = iAtoms[i].distance(query);
if( distance<cutoff)
return true;
}
if (jAtoms!=null) {
for( int i : jIndices ) {
double distance = jAtoms[i].distance(query);
if( distance<cutoff)
return true;
}
}
return false;
} | java | public boolean hasContactToAtom(Point3d[] iAtoms, Point3d[] jAtoms, Point3d query, double cutoff) {
for( int i : iIndices ) {
double distance = iAtoms[i].distance(query);
if( distance<cutoff)
return true;
}
if (jAtoms!=null) {
for( int i : jIndices ) {
double distance = jAtoms[i].distance(query);
if( distance<cutoff)
return true;
}
}
return false;
} | [
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32,206 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentJmolDisplay.java | MultipleAlignmentJmolDisplay.showMultipleAligmentPanel | public static void showMultipleAligmentPanel(MultipleAlignment multAln,
AbstractAlignmentJmol jmol) throws StructureException {
MultipleAligPanel me = new MultipleAligPanel(multAln, jmol);
JFrame frame = new JFrame();
frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
frame.setTitle(jmol.getTitle());
me.setPreferredSize(new Dimension(
me.getCoordManager().getPreferredWidth() ,
me.getCoordManager().getPreferredHeight()));
JMenuBar menu = MenuCreator.getAlignmentPanelMenu(
frame,me,null, multAln);
frame.setJMenuBar(menu);
JScrollPane scroll = new JScrollPane(me);
scroll.setAutoscrolls(true);
MultipleStatusDisplay status = new MultipleStatusDisplay(me);
me.addAlignmentPositionListener(status);
Box vBox = Box.createVerticalBox();
vBox.add(scroll);
vBox.add(status);
frame.getContentPane().add(vBox);
frame.pack();
frame.setVisible(true);
frame.addWindowListener(me);
frame.addWindowListener(status);
} | java | public static void showMultipleAligmentPanel(MultipleAlignment multAln,
AbstractAlignmentJmol jmol) throws StructureException {
MultipleAligPanel me = new MultipleAligPanel(multAln, jmol);
JFrame frame = new JFrame();
frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
frame.setTitle(jmol.getTitle());
me.setPreferredSize(new Dimension(
me.getCoordManager().getPreferredWidth() ,
me.getCoordManager().getPreferredHeight()));
JMenuBar menu = MenuCreator.getAlignmentPanelMenu(
frame,me,null, multAln);
frame.setJMenuBar(menu);
JScrollPane scroll = new JScrollPane(me);
scroll.setAutoscrolls(true);
MultipleStatusDisplay status = new MultipleStatusDisplay(me);
me.addAlignmentPositionListener(status);
Box vBox = Box.createVerticalBox();
vBox.add(scroll);
vBox.add(status);
frame.getContentPane().add(vBox);
frame.pack();
frame.setVisible(true);
frame.addWindowListener(me);
frame.addWindowListener(status);
} | [
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@param multAln
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentJmolDisplay.java#L105-L137 |
32,207 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentJmolDisplay.java | MultipleAlignmentJmolDisplay.display | public static MultipleAlignmentJmol display(MultipleAlignment multAln)
throws StructureException {
List<Atom[]> rotatedAtoms = MultipleAlignmentDisplay.getRotatedAtoms(multAln);
MultipleAlignmentJmol jmol =
new MultipleAlignmentJmol(multAln, rotatedAtoms);
jmol.setTitle(jmol.getStructure().getPDBHeader().getTitle());
return jmol;
} | java | public static MultipleAlignmentJmol display(MultipleAlignment multAln)
throws StructureException {
List<Atom[]> rotatedAtoms = MultipleAlignmentDisplay.getRotatedAtoms(multAln);
MultipleAlignmentJmol jmol =
new MultipleAlignmentJmol(multAln, rotatedAtoms);
jmol.setTitle(jmol.getStructure().getPDBHeader().getTitle());
return jmol;
} | [
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New structures are downloaded if they were
not cached in the alignment and they are entirely
transformed here with the superposition information
in the Multiple Alignment.
@param multAln
@return MultipleAlignmentJmol instance
@throws StructureException | [
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32,208 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/domain/LocalProteinDomainParser.java | LocalProteinDomainParser.suggestDomains | public static List<Domain> suggestDomains(Structure s) throws StructureException{
Atom[] ca = StructureTools.getRepresentativeAtomArray(s);
return suggestDomains(ca);
} | java | public static List<Domain> suggestDomains(Structure s) throws StructureException{
Atom[] ca = StructureTools.getRepresentativeAtomArray(s);
return suggestDomains(ca);
} | [
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... | Suggest domains for a protein structure
@param s the protein structure
@return a list of possible domains
@throws StructureException | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/LocalProteinDomainParser.java#L65-L70 |
32,209 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/domain/LocalProteinDomainParser.java | LocalProteinDomainParser.suggestDomains | public static List<Domain> suggestDomains(Atom[] ca) throws StructureException{
GetDistanceMatrix distMaxCalculator = new GetDistanceMatrix();
PDPDistanceMatrix pdpMatrix = distMaxCalculator.getDistanceMatrix(ca);
Domain dom = new Domain();
Chain c = ca[0].getGroup().getChain();
dom.setId("D"+c.getStructure().getPDBCode()+c.getId()+"1");
dom.setSize(ca.length);
dom.setNseg(1);
dom.getSegmentAtPos(0).setFrom(0);
dom.getSegmentAtPos(0).setTo(ca.length-1);
CutSites cutSites = new CutSites();
// Do the initial splitting
CutDomain cutDomain = new CutDomain(ca,pdpMatrix);
cutDomain.cutDomain(dom, cutSites, pdpMatrix);
List<Domain> domains = cutDomain.getDomains();
//
domains = ClusterDomains.cluster(domains, pdpMatrix);
ShortSegmentRemover.cleanup(domains);
return domains;
} | java | public static List<Domain> suggestDomains(Atom[] ca) throws StructureException{
GetDistanceMatrix distMaxCalculator = new GetDistanceMatrix();
PDPDistanceMatrix pdpMatrix = distMaxCalculator.getDistanceMatrix(ca);
Domain dom = new Domain();
Chain c = ca[0].getGroup().getChain();
dom.setId("D"+c.getStructure().getPDBCode()+c.getId()+"1");
dom.setSize(ca.length);
dom.setNseg(1);
dom.getSegmentAtPos(0).setFrom(0);
dom.getSegmentAtPos(0).setTo(ca.length-1);
CutSites cutSites = new CutSites();
// Do the initial splitting
CutDomain cutDomain = new CutDomain(ca,pdpMatrix);
cutDomain.cutDomain(dom, cutSites, pdpMatrix);
List<Domain> domains = cutDomain.getDomains();
//
domains = ClusterDomains.cluster(domains, pdpMatrix);
ShortSegmentRemover.cleanup(domains);
return domains;
} | [
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@param ca an array of Calpha atoms
@return a list of possible domains
@throws StructureException | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/LocalProteinDomainParser.java#L79-L111 |
32,210 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/GuiWrapper.java | GuiWrapper.showStructure | public static void showStructure(Structure structure)
throws ClassNotFoundException, NoSuchMethodException,
InvocationTargetException, IllegalAccessException, InstantiationException{
Class<?> structureAlignmentJmol = Class.forName(strucAligJmol);
Object strucAligJ = structureAlignmentJmol.newInstance();
Method setS = structureAlignmentJmol.getMethod("setStructure", new Class[] {Structure.class});
setS.invoke(strucAligJ,structure);
} | java | public static void showStructure(Structure structure)
throws ClassNotFoundException, NoSuchMethodException,
InvocationTargetException, IllegalAccessException, InstantiationException{
Class<?> structureAlignmentJmol = Class.forName(strucAligJmol);
Object strucAligJ = structureAlignmentJmol.newInstance();
Method setS = structureAlignmentJmol.getMethod("setStructure", new Class[] {Structure.class});
setS.invoke(strucAligJ,structure);
} | [
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... | Shows a structure in Jmol
@since 3.0.5 | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/GuiWrapper.java#L99-L110 |
32,211 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java | AtomCache.notifyShutdown | public void notifyShutdown() {
// System.out.println(" AtomCache got notify shutdown..");
if (pdpprovider != null) {
if (pdpprovider instanceof RemotePDPProvider) {
RemotePDPProvider remotePDP = (RemotePDPProvider) pdpprovider;
remotePDP.flushCache();
}
}
// todo: use a SCOP implementation that is backed by SerializableCache
ScopDatabase scopInstallation = ScopFactory.getSCOP();
if (scopInstallation != null) {
if (scopInstallation instanceof CachedRemoteScopInstallation) {
CachedRemoteScopInstallation cacheScop = (CachedRemoteScopInstallation) scopInstallation;
cacheScop.flushCache();
}
}
} | java | public void notifyShutdown() {
// System.out.println(" AtomCache got notify shutdown..");
if (pdpprovider != null) {
if (pdpprovider instanceof RemotePDPProvider) {
RemotePDPProvider remotePDP = (RemotePDPProvider) pdpprovider;
remotePDP.flushCache();
}
}
// todo: use a SCOP implementation that is backed by SerializableCache
ScopDatabase scopInstallation = ScopFactory.getSCOP();
if (scopInstallation != null) {
if (scopInstallation instanceof CachedRemoteScopInstallation) {
CachedRemoteScopInstallation cacheScop = (CachedRemoteScopInstallation) scopInstallation;
cacheScop.flushCache();
}
}
} | [
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32,212 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java | AtomCache.getStructureForPdbId | public Structure getStructureForPdbId(String pdbId) throws IOException, StructureException {
if(pdbId == null)
return null;
if(pdbId.length() != 4) {
throw new StructureException("Unrecognized PDB ID: "+pdbId);
}
while (checkLoading(pdbId)) {
// waiting for loading to be finished...
try {
Thread.sleep(100);
} catch (InterruptedException e) {
logger.error(e.getMessage());
}
}
Structure s;
if (useMmtf) {
logger.debug("loading from mmtf");
s = loadStructureFromMmtfByPdbId(pdbId);
}
else if (useMmCif) {
logger.debug("loading from mmcif");
s = loadStructureFromCifByPdbId(pdbId);
} else {
logger.debug("loading from pdb");
s = loadStructureFromPdbByPdbId(pdbId);
}
return s;
} | java | public Structure getStructureForPdbId(String pdbId) throws IOException, StructureException {
if(pdbId == null)
return null;
if(pdbId.length() != 4) {
throw new StructureException("Unrecognized PDB ID: "+pdbId);
}
while (checkLoading(pdbId)) {
// waiting for loading to be finished...
try {
Thread.sleep(100);
} catch (InterruptedException e) {
logger.error(e.getMessage());
}
}
Structure s;
if (useMmtf) {
logger.debug("loading from mmtf");
s = loadStructureFromMmtfByPdbId(pdbId);
}
else if (useMmCif) {
logger.debug("loading from mmcif");
s = loadStructureFromCifByPdbId(pdbId);
} else {
logger.debug("loading from pdb");
s = loadStructureFromPdbByPdbId(pdbId);
}
return s;
} | [
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... | Loads a structure directly by PDB ID
@param pdbId
@return
@throws IOException
@throws StructureException | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java#L867-L897 |
32,213 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DotPlotPanel.java | DotPlotPanel.showDotPlotJFrame | private static JFrame showDotPlotJFrame(AFPChain afpChain ) {
DotPlotPanel dotplot = new DotPlotPanel(afpChain);
//Create JFrame
String title = String.format("Dot plot of %s vs. %s", afpChain.getName1(),afpChain.getName2());
// Create window
JFrame frame = new JFrame(title);
frame.addWindowListener(new WindowAdapter(){
@Override
public void windowClosing(WindowEvent e){
JFrame f = (JFrame) e.getSource();
f.setVisible(false);
f.dispose();
}
});
frame.getContentPane().add(dotplot);
frame.pack();
frame.setVisible(true);
return frame;
} | java | private static JFrame showDotPlotJFrame(AFPChain afpChain ) {
DotPlotPanel dotplot = new DotPlotPanel(afpChain);
//Create JFrame
String title = String.format("Dot plot of %s vs. %s", afpChain.getName1(),afpChain.getName2());
// Create window
JFrame frame = new JFrame(title);
frame.addWindowListener(new WindowAdapter(){
@Override
public void windowClosing(WindowEvent e){
JFrame f = (JFrame) e.getSource();
f.setVisible(false);
f.dispose();
}
});
frame.getContentPane().add(dotplot);
frame.pack();
frame.setVisible(true);
return frame;
} | [
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32,214 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/SSBondImpl.java | SSBondImpl.toPDB | @Override
public void toPDB(StringBuffer buf){
/*12 - 14 LString(3) "CYS" Residue name.
16 Character chainID1 Chain identifier.
18 - 21 Integer seqNum1 Residue sequence number.
22 AChar icode1 Insertion code.
26 - 28 LString(3) "CYS" Residue name.
30 Character chainID2 Chain identifier.
32 - 35 Integer seqNum2 Residue sequence number.
36 AChar icode2 Insertion code.
60 - 65 SymOP sym1 Symmetry oper for 1st resid
67 - 72 SymOP sym2 Symmetry oper for 2nd resid
*/
//01234567890123456789012345678901234567890123456789012345678901234567890123456789
//SSBOND 1 CYS 5 CYS 55 5PTI 67
//SSBOND 2 CYS 14 CYS 38
//SSBOND 3 CYS 30 CYS 51
buf.append("SSBOND ");
buf.append(String.format("%3d", serNum));
buf.append(String.format(" CYS %s %4s%1s ", chainID1, resnum1, insCode1));
buf.append(String.format(" CYS %s %4s%1s ", chainID2, resnum2, insCode2));
} | java | @Override
public void toPDB(StringBuffer buf){
/*12 - 14 LString(3) "CYS" Residue name.
16 Character chainID1 Chain identifier.
18 - 21 Integer seqNum1 Residue sequence number.
22 AChar icode1 Insertion code.
26 - 28 LString(3) "CYS" Residue name.
30 Character chainID2 Chain identifier.
32 - 35 Integer seqNum2 Residue sequence number.
36 AChar icode2 Insertion code.
60 - 65 SymOP sym1 Symmetry oper for 1st resid
67 - 72 SymOP sym2 Symmetry oper for 2nd resid
*/
//01234567890123456789012345678901234567890123456789012345678901234567890123456789
//SSBOND 1 CYS 5 CYS 55 5PTI 67
//SSBOND 2 CYS 14 CYS 38
//SSBOND 3 CYS 30 CYS 51
buf.append("SSBOND ");
buf.append(String.format("%3d", serNum));
buf.append(String.format(" CYS %s %4s%1s ", chainID1, resnum1, insCode1));
buf.append(String.format(" CYS %s %4s%1s ", chainID2, resnum2, insCode2));
} | [
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32,215 | biojava/biojava | biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KaplanMeierFigure.java | KaplanMeierFigure.getSurvivalTimePercentile | public Double getSurvivalTimePercentile(String group, double percentile) {
StrataInfo si = sfi.getStrataInfoHashMap().get(group);
ArrayList<Double> percentage = si.getSurv();
Integer percentileIndex = null;
for (int i = 0; i < percentage.size(); i++) {
if (percentage.get(i) == percentile) {
if (i + 1 < percentage.size()) {
percentileIndex = i + 1;
}
break;
} else if (percentage.get(i) < percentile) {
percentileIndex = i;
break;
}
}
if (percentileIndex != null) {
return si.getTime().get(percentileIndex);
} else {
return null;
}
} | java | public Double getSurvivalTimePercentile(String group, double percentile) {
StrataInfo si = sfi.getStrataInfoHashMap().get(group);
ArrayList<Double> percentage = si.getSurv();
Integer percentileIndex = null;
for (int i = 0; i < percentage.size(); i++) {
if (percentage.get(i) == percentile) {
if (i + 1 < percentage.size()) {
percentileIndex = i + 1;
}
break;
} else if (percentage.get(i) < percentile) {
percentileIndex = i;
break;
}
}
if (percentileIndex != null) {
return si.getTime().get(percentileIndex);
} else {
return null;
}
} | [
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32,216 | biojava/biojava | biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KaplanMeierFigure.java | KaplanMeierFigure.setSurvivalData | public void setSurvivalData(ArrayList<String> title, SurvFitInfo sfi, Double userSetMaxTime) {
this.title = title;
LinkedHashMap<String, StrataInfo> strataInfoHashMap = sfi.getStrataInfoHashMap();
Double mTime = null;
for (StrataInfo si : strataInfoHashMap.values()) {
for (double t : si.getTime()) {
if (mTime == null || t > mTime) {
mTime = t;
}
}
}
int evenCheck = Math.round(mTime.floatValue());
if (evenCheck % 2 == 1) {
evenCheck = evenCheck + 1;
}
this.maxTime = evenCheck;
if (userSetMaxTime != null && userSetMaxTime > maxTime) {
this.maxTime = userSetMaxTime;
}
this.sfi = sfi;
if (sfi.getStrataInfoHashMap().size() == 1) {
return;
}
this.repaint();
} | java | public void setSurvivalData(ArrayList<String> title, SurvFitInfo sfi, Double userSetMaxTime) {
this.title = title;
LinkedHashMap<String, StrataInfo> strataInfoHashMap = sfi.getStrataInfoHashMap();
Double mTime = null;
for (StrataInfo si : strataInfoHashMap.values()) {
for (double t : si.getTime()) {
if (mTime == null || t > mTime) {
mTime = t;
}
}
}
int evenCheck = Math.round(mTime.floatValue());
if (evenCheck % 2 == 1) {
evenCheck = evenCheck + 1;
}
this.maxTime = evenCheck;
if (userSetMaxTime != null && userSetMaxTime > maxTime) {
this.maxTime = userSetMaxTime;
}
this.sfi = sfi;
if (sfi.getStrataInfoHashMap().size() == 1) {
return;
}
this.repaint();
} | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KaplanMeierFigure.java#L253-L279 |
32,217 | biojava/biojava | biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KaplanMeierFigure.java | KaplanMeierFigure.setSurvivalData | public void setSurvivalData(ArrayList<String> title, LinkedHashMap<String, ArrayList<CensorStatus>> survivalData, Boolean useWeighted) throws Exception {
this.setSurvivalData(title, survivalData, null, useWeighted);
} | java | public void setSurvivalData(ArrayList<String> title, LinkedHashMap<String, ArrayList<CensorStatus>> survivalData, Boolean useWeighted) throws Exception {
this.setSurvivalData(title, survivalData, null, useWeighted);
} | [
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32,218 | biojava/biojava | biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KaplanMeierFigure.java | KaplanMeierFigure.saveSurvivalData | public void saveSurvivalData(String fileName) throws Exception {
FileWriter fw = new FileWriter(fileName);
fw.write("index\tTIME\tSTATUS\tGROUP\r\n");
int index = 0;
for (String group : survivalData.keySet()) {
ArrayList<CensorStatus> sd = survivalData.get(group);
for (CensorStatus cs : sd) {
String line = index + "\t" + cs.time + "\t" + cs.censored + "\t" + cs.group + "\r\n";
index++;
fw.write(line);
}
}
fw.close();
} | java | public void saveSurvivalData(String fileName) throws Exception {
FileWriter fw = new FileWriter(fileName);
fw.write("index\tTIME\tSTATUS\tGROUP\r\n");
int index = 0;
for (String group : survivalData.keySet()) {
ArrayList<CensorStatus> sd = survivalData.get(group);
for (CensorStatus cs : sd) {
String line = index + "\t" + cs.time + "\t" + cs.censored + "\t" + cs.group + "\r\n";
index++;
fw.write(line);
}
}
fw.close();
} | [
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32,219 | biojava/biojava | biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KaplanMeierFigure.java | KaplanMeierFigure.getTimeX | private int getTimeX(double value) {
double d = left + (((right - left) * value) / (maxTime - minTime));
return (int) d;
} | java | private int getTimeX(double value) {
double d = left + (((right - left) * value) / (maxTime - minTime));
return (int) d;
} | [
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32,220 | biojava/biojava | biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KaplanMeierFigure.java | KaplanMeierFigure.getPercentageY | private int getPercentageY(double value) {
value = 1.0 - value;
double d = top + (((bottom - top) * value) / (maxPercentage - minPercentage));
return (int) d;
} | java | private int getPercentageY(double value) {
value = 1.0 - value;
double d = top + (((bottom - top) * value) / (maxPercentage - minPercentage));
return (int) d;
} | [
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32,221 | biojava/biojava | biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KaplanMeierFigure.java | KaplanMeierFigure.savePNGKMNumRisk | public void savePNGKMNumRisk(String fileName) {
if (fileName.startsWith("null") || fileName.startsWith("Null") || fileName.startsWith("NULL")) {
return;
}
this.fileName = fileName;
NumbersAtRiskPanel numbersAtRiskPanel = new NumbersAtRiskPanel();
numbersAtRiskPanel.setKaplanMeierFigure(this);
numbersAtRiskPanel.setSize(this.getWidth(), numbersAtRiskPanel.getHeight());
BufferedImage imageKM = new BufferedImage(this.getWidth(), this.getHeight(), BufferedImage.TYPE_INT_RGB);
Graphics2D graphics2D = imageKM.createGraphics();
this.paint(graphics2D);
BufferedImage imageNumRisk = new BufferedImage(numbersAtRiskPanel.getWidth(), numbersAtRiskPanel.getHeight(), BufferedImage.TYPE_INT_RGB);
Graphics2D graphics2DNumRisk = imageNumRisk.createGraphics();
numbersAtRiskPanel.paint(graphics2DNumRisk);
BufferedImage image = new BufferedImage(numbersAtRiskPanel.getWidth(), numbersAtRiskPanel.getHeight() + this.getHeight(), BufferedImage.TYPE_INT_RGB);
Graphics2D g = image.createGraphics();
g.drawImage(imageKM, 0, 0, null);
g.drawImage(imageNumRisk, 0, this.getHeight(), null);
try {
ImageIO.write(image, "png", new File(fileName));
} catch (Exception ex) {
ex.printStackTrace();
}
} | java | public void savePNGKMNumRisk(String fileName) {
if (fileName.startsWith("null") || fileName.startsWith("Null") || fileName.startsWith("NULL")) {
return;
}
this.fileName = fileName;
NumbersAtRiskPanel numbersAtRiskPanel = new NumbersAtRiskPanel();
numbersAtRiskPanel.setKaplanMeierFigure(this);
numbersAtRiskPanel.setSize(this.getWidth(), numbersAtRiskPanel.getHeight());
BufferedImage imageKM = new BufferedImage(this.getWidth(), this.getHeight(), BufferedImage.TYPE_INT_RGB);
Graphics2D graphics2D = imageKM.createGraphics();
this.paint(graphics2D);
BufferedImage imageNumRisk = new BufferedImage(numbersAtRiskPanel.getWidth(), numbersAtRiskPanel.getHeight(), BufferedImage.TYPE_INT_RGB);
Graphics2D graphics2DNumRisk = imageNumRisk.createGraphics();
numbersAtRiskPanel.paint(graphics2DNumRisk);
BufferedImage image = new BufferedImage(numbersAtRiskPanel.getWidth(), numbersAtRiskPanel.getHeight() + this.getHeight(), BufferedImage.TYPE_INT_RGB);
Graphics2D g = image.createGraphics();
g.drawImage(imageKM, 0, 0, null);
g.drawImage(imageNumRisk, 0, this.getHeight(), null);
try {
ImageIO.write(image, "png", new File(fileName));
} catch (Exception ex) {
ex.printStackTrace();
}
} | [
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32,222 | spring-cloud/spring-cloud-contract | spring-cloud-contract-stub-runner/src/main/java/org/springframework/cloud/contract/stubrunner/spring/StubRunnerConfiguration.java | StubRunnerConfiguration.batchStubRunner | @Bean
public BatchStubRunner batchStubRunner() {
StubRunnerOptionsBuilder builder = builder();
if (this.props.getProxyHost() != null) {
builder.withProxy(this.props.getProxyHost(), this.props.getProxyPort());
}
StubRunnerOptions stubRunnerOptions = builder.build();
BatchStubRunner batchStubRunner = new BatchStubRunnerFactory(stubRunnerOptions,
this.provider.get(stubRunnerOptions),
this.contractVerifierMessaging != null ? this.contractVerifierMessaging
: new NoOpStubMessages()).buildBatchStubRunner();
// TODO: Consider running it in a separate thread
RunningStubs runningStubs = batchStubRunner.runStubs();
registerPort(runningStubs);
return batchStubRunner;
} | java | @Bean
public BatchStubRunner batchStubRunner() {
StubRunnerOptionsBuilder builder = builder();
if (this.props.getProxyHost() != null) {
builder.withProxy(this.props.getProxyHost(), this.props.getProxyPort());
}
StubRunnerOptions stubRunnerOptions = builder.build();
BatchStubRunner batchStubRunner = new BatchStubRunnerFactory(stubRunnerOptions,
this.provider.get(stubRunnerOptions),
this.contractVerifierMessaging != null ? this.contractVerifierMessaging
: new NoOpStubMessages()).buildBatchStubRunner();
// TODO: Consider running it in a separate thread
RunningStubs runningStubs = batchStubRunner.runStubs();
registerPort(runningStubs);
return batchStubRunner;
} | [
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32,223 | spring-cloud/spring-cloud-contract | spring-cloud-contract-stub-runner/src/main/java/org/springframework/cloud/contract/stubrunner/ContractProjectUpdater.java | ContractProjectUpdater.updateContractProject | public void updateContractProject(String projectName, Path rootStubsFolder) {
File clonedRepo = this.gitContractsRepo
.clonedRepo(this.stubRunnerOptions.stubRepositoryRoot);
GitStubDownloaderProperties properties = new GitStubDownloaderProperties(
this.stubRunnerOptions.stubRepositoryRoot, this.stubRunnerOptions);
copyStubs(projectName, rootStubsFolder, clonedRepo);
GitRepo gitRepo = new GitRepo(clonedRepo, properties);
String msg = StubRunnerPropertyUtils
.getProperty(this.stubRunnerOptions.getProperties(), GIT_COMMIT_MESSAGE);
GitRepo.CommitResult commit = gitRepo.commit(clonedRepo,
commitMessage(projectName, msg));
if (commit == GitRepo.CommitResult.EMPTY) {
log.info("There were no changes to commit. Won't push the changes");
return;
}
String attempts = StubRunnerPropertyUtils.getProperty(
this.stubRunnerOptions.getProperties(), GIT_ATTEMPTS_NO_PROP);
int intAttempts = StringUtils.hasText(attempts) ? Integer.parseInt(attempts)
: DEFAULT_ATTEMPTS_NO;
String wait = StubRunnerPropertyUtils.getProperty(
this.stubRunnerOptions.getProperties(), GIT_WAIT_BETWEEN_ATTEMPTS);
long longWait = StringUtils.hasText(wait) ? Long.parseLong(wait)
: DEFAULT_WAIT_BETWEEN_ATTEMPTS;
tryToPushCurrentBranch(clonedRepo, gitRepo, intAttempts, longWait);
} | java | public void updateContractProject(String projectName, Path rootStubsFolder) {
File clonedRepo = this.gitContractsRepo
.clonedRepo(this.stubRunnerOptions.stubRepositoryRoot);
GitStubDownloaderProperties properties = new GitStubDownloaderProperties(
this.stubRunnerOptions.stubRepositoryRoot, this.stubRunnerOptions);
copyStubs(projectName, rootStubsFolder, clonedRepo);
GitRepo gitRepo = new GitRepo(clonedRepo, properties);
String msg = StubRunnerPropertyUtils
.getProperty(this.stubRunnerOptions.getProperties(), GIT_COMMIT_MESSAGE);
GitRepo.CommitResult commit = gitRepo.commit(clonedRepo,
commitMessage(projectName, msg));
if (commit == GitRepo.CommitResult.EMPTY) {
log.info("There were no changes to commit. Won't push the changes");
return;
}
String attempts = StubRunnerPropertyUtils.getProperty(
this.stubRunnerOptions.getProperties(), GIT_ATTEMPTS_NO_PROP);
int intAttempts = StringUtils.hasText(attempts) ? Integer.parseInt(attempts)
: DEFAULT_ATTEMPTS_NO;
String wait = StubRunnerPropertyUtils.getProperty(
this.stubRunnerOptions.getProperties(), GIT_WAIT_BETWEEN_ATTEMPTS);
long longWait = StringUtils.hasText(wait) ? Long.parseLong(wait)
: DEFAULT_WAIT_BETWEEN_ATTEMPTS;
tryToPushCurrentBranch(clonedRepo, gitRepo, intAttempts, longWait);
} | [
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32,224 | spring-cloud/spring-cloud-contract | spring-cloud-contract-spec/src/main/groovy/repackaged/nl/flotsam/xeger/Xeger.java | Xeger.getRandomInt | static int getRandomInt(int min, int max, Random random) {
// Use random.nextInt as it guarantees a uniform distribution
int maxForRandom = max - min + 1;
return random.nextInt(maxForRandom) + min;
} | java | static int getRandomInt(int min, int max, Random random) {
// Use random.nextInt as it guarantees a uniform distribution
int maxForRandom = max - min + 1;
return random.nextInt(maxForRandom) + min;
} | [
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32,225 | spring-cloud/spring-cloud-contract | spring-cloud-contract-spec/src/main/groovy/repackaged/nl/flotsam/xeger/Xeger.java | Xeger.generate | public String generate() {
StringBuilder builder = new StringBuilder();
int counter = 0;
generate(builder, this.automaton.getInitialState(), counter);
return builder.toString();
} | java | public String generate() {
StringBuilder builder = new StringBuilder();
int counter = 0;
generate(builder, this.automaton.getInitialState(), counter);
return builder.toString();
} | [
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32,226 | spring-cloud/spring-cloud-contract | spring-cloud-contract-stub-runner/src/main/java/org/springframework/cloud/contract/stubrunner/AetherFactories.java | AetherFactories.fromSystemPropOrEnv | private static String fromSystemPropOrEnv(String prop) {
String resolvedProp = System.getProperty(prop);
if (StringUtils.hasText(resolvedProp)) {
return resolvedProp;
}
return System.getenv(prop);
} | java | private static String fromSystemPropOrEnv(String prop) {
String resolvedProp = System.getProperty(prop);
if (StringUtils.hasText(resolvedProp)) {
return resolvedProp;
}
return System.getenv(prop);
} | [
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32,227 | spring-cloud/spring-cloud-contract | spring-cloud-contract-wiremock/src/main/java/org/springframework/cloud/contract/wiremock/restdocs/ContractResultHandler.java | WireMockHttpServletRequestAdapter.getBody | @Override
public byte[] getBody() {
if (this.cachedBody == null || this.cachedBody.length == 0) {
try {
if (this.request instanceof MockHttpServletRequest) {
this.cachedBody = ((MockHttpServletRequest) this.request)
.getContentAsByteArray();
return this.cachedBody;
}
byte[] body = toByteArray(this.request.getInputStream());
boolean isGzipped = hasGzipEncoding() || Gzip.isGzipped(body);
this.cachedBody = isGzipped ? Gzip.unGzip(body) : body;
}
catch (IOException ioe) {
throw new RuntimeException(ioe);
}
}
return this.cachedBody;
} | java | @Override
public byte[] getBody() {
if (this.cachedBody == null || this.cachedBody.length == 0) {
try {
if (this.request instanceof MockHttpServletRequest) {
this.cachedBody = ((MockHttpServletRequest) this.request)
.getContentAsByteArray();
return this.cachedBody;
}
byte[] body = toByteArray(this.request.getInputStream());
boolean isGzipped = hasGzipEncoding() || Gzip.isGzipped(body);
this.cachedBody = isGzipped ? Gzip.unGzip(body) : body;
}
catch (IOException ioe) {
throw new RuntimeException(ioe);
}
}
return this.cachedBody;
} | [
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32,228 | spring-cloud/spring-cloud-contract | spring-cloud-contract-stub-runner/src/main/java/org/springframework/cloud/contract/stubrunner/GitRepo.java | GitRepo.cloneProject | File cloneProject(URI projectUri) {
try {
log.info("Cloning repo from [" + projectUri + "] to [" + this.basedir + "]");
Git git = cloneToBasedir(projectUri, this.basedir);
if (git != null) {
git.close();
}
File clonedRepo = git.getRepository().getWorkTree();
log.info("Cloned repo to [" + clonedRepo + "]");
return clonedRepo;
}
catch (Exception e) {
throw new IllegalStateException("Exception occurred while cloning repo", e);
}
} | java | File cloneProject(URI projectUri) {
try {
log.info("Cloning repo from [" + projectUri + "] to [" + this.basedir + "]");
Git git = cloneToBasedir(projectUri, this.basedir);
if (git != null) {
git.close();
}
File clonedRepo = git.getRepository().getWorkTree();
log.info("Cloned repo to [" + clonedRepo + "]");
return clonedRepo;
}
catch (Exception e) {
throw new IllegalStateException("Exception occurred while cloning repo", e);
}
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32,229 | spring-cloud/spring-cloud-contract | spring-cloud-contract-stub-runner/src/main/java/org/springframework/cloud/contract/stubrunner/GitRepo.java | GitRepo.checkout | void checkout(File project, String branch) {
try {
String currentBranch = currentBranch(project);
if (currentBranch.equals(branch)) {
log.info("Won't check out the same branch. Skipping");
return;
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checkoutBranch(project, branch);
log.info("Successfully checked out the branch [" + branch + "]");
}
catch (Exception e) {
throw new IllegalStateException(e);
}
} | java | void checkout(File project, String branch) {
try {
String currentBranch = currentBranch(project);
if (currentBranch.equals(branch)) {
log.info("Won't check out the same branch. Skipping");
return;
}
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32,230 | spring-cloud/spring-cloud-contract | spring-cloud-contract-stub-runner/src/main/java/org/springframework/cloud/contract/stubrunner/GitRepo.java | GitRepo.pull | void pull(File project) {
try {
try (Git git = this.gitFactory.open(project)) {
PullCommand command = this.gitFactory.pull(git);
command.setRebase(true).call();
}
}
catch (Exception e) {
throw new IllegalStateException(e);
}
} | java | void pull(File project) {
try {
try (Git git = this.gitFactory.open(project)) {
PullCommand command = this.gitFactory.pull(git);
command.setRebase(true).call();
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32,231 | spring-cloud/spring-cloud-contract | spring-cloud-contract-stub-runner/src/main/java/org/springframework/cloud/contract/stubrunner/GitRepo.java | GitRepo.commit | CommitResult commit(File project, String message) {
try (Git git = this.gitFactory.open(file(project))) {
git.add().addFilepattern(".").call();
git.commit().setAllowEmpty(false).setMessage(message).call();
log.info("Commited successfully with message [" + message + "]");
return CommitResult.SUCCESSFUL;
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log.info("There were no changes detected. Will not commit an empty commit");
return CommitResult.EMPTY;
}
catch (Exception e) {
throw new IllegalStateException(e);
}
} | java | CommitResult commit(File project, String message) {
try (Git git = this.gitFactory.open(file(project))) {
git.add().addFilepattern(".").call();
git.commit().setAllowEmpty(false).setMessage(message).call();
log.info("Commited successfully with message [" + message + "]");
return CommitResult.SUCCESSFUL;
}
catch (EmptyCommitException e) {
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32,232 | spring-cloud/spring-cloud-contract | spring-cloud-contract-stub-runner/src/main/java/org/springframework/cloud/contract/stubrunner/GitRepo.java | GitRepo.pushCurrentBranch | void pushCurrentBranch(File project) {
try (Git git = this.gitFactory.open(file(project))) {
this.gitFactory.push(git).call();
}
catch (Exception e) {
throw new IllegalStateException(e);
}
} | java | void pushCurrentBranch(File project) {
try (Git git = this.gitFactory.open(file(project))) {
this.gitFactory.push(git).call();
}
catch (Exception e) {
throw new IllegalStateException(e);
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32,233 | spring-cloud/spring-cloud-contract | spring-cloud-contract-stub-runner/src/main/java/org/springframework/cloud/contract/stubrunner/provider/wiremock/WireMockHttpServerStub.java | WireMockHttpServerStub.helpers | @Deprecated
protected Map<String, Helper> helpers() {
Map<String, Helper> helpers = new HashMap<>();
helpers.put(HandlebarsJsonPathHelper.NAME, new HandlebarsJsonPathHelper());
helpers.put(HandlebarsEscapeHelper.NAME, new HandlebarsEscapeHelper());
return helpers;
} | java | @Deprecated
protected Map<String, Helper> helpers() {
Map<String, Helper> helpers = new HashMap<>();
helpers.put(HandlebarsJsonPathHelper.NAME, new HandlebarsJsonPathHelper());
helpers.put(HandlebarsEscapeHelper.NAME, new HandlebarsEscapeHelper());
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32,234 | spring-cloud/spring-cloud-contract | spring-cloud-contract-verifier/src/main/java/org/springframework/cloud/contract/verifier/util/ContractVerifierUtil.java | ContractVerifierUtil.fileToBytes | public static byte[] fileToBytes(Object testClass, String relativePath) {
try {
URL url = testClass.getClass().getResource(relativePath);
if (url == null) {
throw new FileNotFoundException(relativePath);
}
return Files.readAllBytes(Paths.get(url.toURI()));
}
catch (IOException | URISyntaxException ex) {
throw new IllegalStateException(ex);
}
} | java | public static byte[] fileToBytes(Object testClass, String relativePath) {
try {
URL url = testClass.getClass().getResource(relativePath);
if (url == null) {
throw new FileNotFoundException(relativePath);
}
return Files.readAllBytes(Paths.get(url.toURI()));
}
catch (IOException | URISyntaxException ex) {
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}
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32,235 | spring-cloud/spring-cloud-contract | spring-cloud-contract-verifier/src/main/java/org/springframework/cloud/contract/verifier/util/ContractVerifierUtil.java | ContractVerifierUtil.valueFromXPath | public static String valueFromXPath(Document parsedXml, String path) {
XPath xPath = XPathFactory.newInstance().newXPath();
try {
return xPath.evaluate(path, parsedXml.getDocumentElement());
}
catch (XPathExpressionException exception) {
LOG.error("Incorrect xpath provided: " + path, exception);
throw new IllegalArgumentException();
}
} | java | public static String valueFromXPath(Document parsedXml, String path) {
XPath xPath = XPathFactory.newInstance().newXPath();
try {
return xPath.evaluate(path, parsedXml.getDocumentElement());
}
catch (XPathExpressionException exception) {
LOG.error("Incorrect xpath provided: " + path, exception);
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}
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32,236 | spring-cloud/spring-cloud-contract | spring-cloud-contract-stub-runner/src/main/java/org/springframework/cloud/contract/stubrunner/ContractDownloader.java | ContractDownloader.unpackedDownloadedContracts | public File unpackedDownloadedContracts(ContractVerifierConfigProperties config) {
File contractsDirectory = unpackAndDownloadContracts();
updatePropertiesWithInclusion(contractsDirectory, config);
return contractsDirectory;
} | java | public File unpackedDownloadedContracts(ContractVerifierConfigProperties config) {
File contractsDirectory = unpackAndDownloadContracts();
updatePropertiesWithInclusion(contractsDirectory, config);
return contractsDirectory;
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32,237 | spring-cloud/spring-cloud-contract | spring-cloud-contract-verifier/src/main/java/org/springframework/cloud/contract/verifier/assertion/CollectionAssert.java | CollectionAssert.allElementsMatch | public CollectionAssert allElementsMatch(String regex) {
isNotNull();
isNotEmpty();
for (Object anActual : this.actual) {
if (anActual == null) {
failWithMessageRelatedToRegex(regex, anActual);
}
String value = anActual.toString();
if (!value.matches(regex)) {
failWithMessageRelatedToRegex(regex, value);
}
}
return this;
} | java | public CollectionAssert allElementsMatch(String regex) {
isNotNull();
isNotEmpty();
for (Object anActual : this.actual) {
if (anActual == null) {
failWithMessageRelatedToRegex(regex, anActual);
}
String value = anActual.toString();
if (!value.matches(regex)) {
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}
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32,238 | spring-cloud/spring-cloud-contract | spring-cloud-contract-verifier/src/main/java/org/springframework/cloud/contract/verifier/assertion/CollectionAssert.java | CollectionAssert.hasFlattenedSizeGreaterThanOrEqualTo | public CollectionAssert hasFlattenedSizeGreaterThanOrEqualTo(int size) {
isNotNull();
int flattenedSize = flattenedSize(0, this.actual);
if (!(flattenedSize >= size)) {
failWithMessage("The flattened size <%s> is not greater or equal to <%s>",
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}
return this;
} | java | public CollectionAssert hasFlattenedSizeGreaterThanOrEqualTo(int size) {
isNotNull();
int flattenedSize = flattenedSize(0, this.actual);
if (!(flattenedSize >= size)) {
failWithMessage("The flattened size <%s> is not greater or equal to <%s>",
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32,239 | spring-cloud/spring-cloud-contract | spring-cloud-contract-verifier/src/main/java/org/springframework/cloud/contract/verifier/assertion/CollectionAssert.java | CollectionAssert.hasFlattenedSizeLessThanOrEqualTo | public CollectionAssert hasFlattenedSizeLessThanOrEqualTo(int size) {
isNotNull();
int flattenedSize = flattenedSize(0, this.actual);
if (!(flattenedSize <= size)) {
failWithMessage("The flattened size <%s> is not less or equal to <%s>",
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}
return this;
} | java | public CollectionAssert hasFlattenedSizeLessThanOrEqualTo(int size) {
isNotNull();
int flattenedSize = flattenedSize(0, this.actual);
if (!(flattenedSize <= size)) {
failWithMessage("The flattened size <%s> is not less or equal to <%s>",
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32,240 | spring-cloud/spring-cloud-contract | spring-cloud-contract-verifier/src/main/java/org/springframework/cloud/contract/verifier/assertion/CollectionAssert.java | CollectionAssert.hasFlattenedSizeBetween | public CollectionAssert hasFlattenedSizeBetween(int lowerBound, int higherBound) {
isNotNull();
int flattenedSize = flattenedSize(0, this.actual);
if (!(flattenedSize >= lowerBound && flattenedSize <= higherBound)) {
failWithMessage("The flattened size <%s> is not between <%s> and <%s>",
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}
return this;
} | java | public CollectionAssert hasFlattenedSizeBetween(int lowerBound, int higherBound) {
isNotNull();
int flattenedSize = flattenedSize(0, this.actual);
if (!(flattenedSize >= lowerBound && flattenedSize <= higherBound)) {
failWithMessage("The flattened size <%s> is not between <%s> and <%s>",
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32,241 | spring-cloud/spring-cloud-contract | spring-cloud-contract-verifier/src/main/java/org/springframework/cloud/contract/verifier/assertion/CollectionAssert.java | CollectionAssert.hasSizeGreaterThanOrEqualTo | public CollectionAssert hasSizeGreaterThanOrEqualTo(int size) {
isNotNull();
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if (!(actualSize >= size)) {
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}
return this;
} | java | public CollectionAssert hasSizeGreaterThanOrEqualTo(int size) {
isNotNull();
int actualSize = size(this.actual);
if (!(actualSize >= size)) {
failWithMessage("The size <%s> is not greater or equal to <%s>", actualSize,
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32,242 | spring-cloud/spring-cloud-contract | spring-cloud-contract-verifier/src/main/java/org/springframework/cloud/contract/verifier/assertion/CollectionAssert.java | CollectionAssert.hasSizeLessThanOrEqualTo | public CollectionAssert hasSizeLessThanOrEqualTo(int size) {
isNotNull();
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failWithMessage("The size <%s> is not less or equal to <%s>", actualSize,
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}
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} | java | public CollectionAssert hasSizeLessThanOrEqualTo(int size) {
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32,243 | spring-cloud/spring-cloud-contract | spring-cloud-contract-verifier/src/main/java/org/springframework/cloud/contract/verifier/assertion/CollectionAssert.java | CollectionAssert.hasSizeBetween | public CollectionAssert hasSizeBetween(int lowerBound, int higherBound) {
isNotNull();
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32,244 | spring-cloud/spring-cloud-contract | spring-cloud-contract-stub-runner/src/main/java/org/springframework/cloud/contract/stubrunner/util/StubsParser.java | StubsParser.fromString | public static List<StubConfiguration> fromString(Collection<String> collection,
String defaultClassifier) {
List<StubConfiguration> stubs = new ArrayList<>();
for (String config : collection) {
if (StringUtils.hasText(config)) {
stubs.add(StubSpecification.parse(config, defaultClassifier).stub);
}
}
return stubs;
} | java | public static List<StubConfiguration> fromString(Collection<String> collection,
String defaultClassifier) {
List<StubConfiguration> stubs = new ArrayList<>();
for (String config : collection) {
if (StringUtils.hasText(config)) {
stubs.add(StubSpecification.parse(config, defaultClassifier).stub);
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32,245 | spring-cloud/spring-cloud-contract | spring-cloud-contract-stub-runner/src/main/java/org/springframework/cloud/contract/stubrunner/StubConfiguration.java | StubConfiguration.groupIdAndArtifactMatches | public boolean groupIdAndArtifactMatches(String ivyNotationAsString) {
String[] parts = ivyNotationFrom(ivyNotationAsString);
String groupId = parts[0];
String artifactId = parts[1];
if (groupId == null) {
return this.artifactId.equals(artifactId);
}
return this.groupId.equals(groupId) && this.artifactId.equals(artifactId);
} | java | public boolean groupIdAndArtifactMatches(String ivyNotationAsString) {
String[] parts = ivyNotationFrom(ivyNotationAsString);
String groupId = parts[0];
String artifactId = parts[1];
if (groupId == null) {
return this.artifactId.equals(artifactId);
}
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32,246 | allure-framework/allure-java | allure-java-commons/src/main/java/io/qameta/allure/util/ServiceLoaderUtils.java | ServiceLoaderUtils.load | public static <T> List<T> load(final Class<T> type, final ClassLoader classLoader) {
final List<T> loaded = new ArrayList<>();
final Iterator<T> iterator = ServiceLoader.load(type, classLoader).iterator();
while (hasNextSafely(iterator)) {
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loaded.add(next);
LOGGER.debug("Found {}", type);
} catch (Exception e) {
LOGGER.error("Could not load {}: {}", type, e);
}
}
return loaded;
} | java | public static <T> List<T> load(final Class<T> type, final ClassLoader classLoader) {
final List<T> loaded = new ArrayList<>();
final Iterator<T> iterator = ServiceLoader.load(type, classLoader).iterator();
while (hasNextSafely(iterator)) {
try {
final T next = iterator.next();
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LOGGER.debug("Found {}", type);
} catch (Exception e) {
LOGGER.error("Could not load {}: {}", type, e);
}
}
return loaded;
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32,247 | allure-framework/allure-java | allure-java-commons/src/main/java/io/qameta/allure/internal/AllureThreadContext.java | AllureThreadContext.start | public void start(final String uuid) {
Objects.requireNonNull(uuid, "step uuid");
context.get().push(uuid);
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Objects.requireNonNull(uuid, "step uuid");
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32,248 | allure-framework/allure-java | allure-java-commons/src/main/java/io/qameta/allure/internal/AllureThreadContext.java | AllureThreadContext.stop | public Optional<String> stop() {
final LinkedList<String> uuids = context.get();
if (!uuids.isEmpty()) {
return Optional.of(uuids.pop());
}
return Optional.empty();
} | java | public Optional<String> stop() {
final LinkedList<String> uuids = context.get();
if (!uuids.isEmpty()) {
return Optional.of(uuids.pop());
}
return Optional.empty();
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32,249 | allure-framework/allure-java | allure-cucumber4-jvm/src/main/java/io/qameta/allure/cucumber4jvm/LabelBuilder.java | LabelBuilder.tryHandleNamedLink | private void tryHandleNamedLink(final String tagString) {
final String namedLinkPatternString = PLAIN_LINK + "\\.(\\w+-?)+=(\\w+(-|_)?)+";
final Pattern namedLinkPattern = Pattern.compile(namedLinkPatternString, Pattern.CASE_INSENSITIVE);
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final String name = tagString.split(COMPOSITE_TAG_DELIMITER)[1];
getScenarioLinks().add(ResultsUtils.createLink(null, name, null, type));
} else {
LOGGER.warn("Composite named tag {} does not match regex {}. Skipping", tagString,
namedLinkPatternString);
}
} | java | private void tryHandleNamedLink(final String tagString) {
final String namedLinkPatternString = PLAIN_LINK + "\\.(\\w+-?)+=(\\w+(-|_)?)+";
final Pattern namedLinkPattern = Pattern.compile(namedLinkPatternString, Pattern.CASE_INSENSITIVE);
if (namedLinkPattern.matcher(tagString).matches()) {
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32,250 | allure-framework/allure-java | allure-java-migration/src/main/java/io/qameta/allure/aspects/Allure1Utils.java | Allure1Utils.getParametersAsString | public static String getParametersAsString(final Object... parameters) {
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final StringBuilder builder = new StringBuilder();
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}
}
return builder.append(']').toString();
} | java | public static String getParametersAsString(final Object... parameters) {
if (parameters == null || parameters.length == 0) {
return "";
}
final StringBuilder builder = new StringBuilder();
builder.append('[');
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32,251 | allure-framework/allure-java | allure-java-commons/src/main/java/io/qameta/allure/AllureLifecycle.java | AllureLifecycle.startPrepareFixture | public void startPrepareFixture(final String containerUuid, final String uuid, final FixtureResult result) {
storage.getContainer(containerUuid).ifPresent(container -> {
synchronized (storage) {
container.getBefores().add(result);
}
});
notifier.beforeFixtureStart(result);
startFixture(uuid, result);
notifier.afterFixtureStart(result);
} | java | public void startPrepareFixture(final String containerUuid, final String uuid, final FixtureResult result) {
storage.getContainer(containerUuid).ifPresent(container -> {
synchronized (storage) {
container.getBefores().add(result);
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startFixture(uuid, result);
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32,252 | allure-framework/allure-java | allure-java-commons/src/main/java/io/qameta/allure/AllureLifecycle.java | AllureLifecycle.startTearDownFixture | public void startTearDownFixture(final String containerUuid, final String uuid, final FixtureResult result) {
storage.getContainer(containerUuid).ifPresent(container -> {
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container.getAfters().add(result);
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});
notifier.beforeFixtureStart(result);
startFixture(uuid, result);
notifier.afterFixtureStart(result);
} | java | public void startTearDownFixture(final String containerUuid, final String uuid, final FixtureResult result) {
storage.getContainer(containerUuid).ifPresent(container -> {
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32,253 | allure-framework/allure-java | allure-java-commons/src/main/java/io/qameta/allure/AllureLifecycle.java | AllureLifecycle.startFixture | private void startFixture(final String uuid, final FixtureResult result) {
storage.put(uuid, result);
result.setStage(Stage.RUNNING);
result.setStart(System.currentTimeMillis());
threadContext.clear();
threadContext.start(uuid);
} | java | private void startFixture(final String uuid, final FixtureResult result) {
storage.put(uuid, result);
result.setStage(Stage.RUNNING);
result.setStart(System.currentTimeMillis());
threadContext.clear();
threadContext.start(uuid);
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32,254 | allure-framework/allure-java | allure-java-commons/src/main/java/io/qameta/allure/AllureLifecycle.java | AllureLifecycle.updateFixture | public void updateFixture(final String uuid, final Consumer<FixtureResult> update) {
final Optional<FixtureResult> found = storage.getFixture(uuid);
if (!found.isPresent()) {
LOGGER.error("Could not update test fixture: test fixture with uuid {} not found", uuid);
return;
}
final FixtureResult fixture = found.get();
notifier.beforeFixtureUpdate(fixture);
update.accept(fixture);
notifier.afterFixtureUpdate(fixture);
} | java | public void updateFixture(final String uuid, final Consumer<FixtureResult> update) {
final Optional<FixtureResult> found = storage.getFixture(uuid);
if (!found.isPresent()) {
LOGGER.error("Could not update test fixture: test fixture with uuid {} not found", uuid);
return;
}
final FixtureResult fixture = found.get();
notifier.beforeFixtureUpdate(fixture);
update.accept(fixture);
notifier.afterFixtureUpdate(fixture);
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32,255 | allure-framework/allure-java | allure-java-commons/src/main/java/io/qameta/allure/AllureLifecycle.java | AllureLifecycle.stopFixture | public void stopFixture(final String uuid) {
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return;
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fixture.setStage(Stage.FINISHED);
fixture.setStop(System.currentTimeMillis());
storage.remove(uuid);
threadContext.clear();
notifier.afterFixtureStop(fixture);
} | java | public void stopFixture(final String uuid) {
final Optional<FixtureResult> found = storage.getFixture(uuid);
if (!found.isPresent()) {
LOGGER.error("Could not stop test fixture: test fixture with uuid {} not found", uuid);
return;
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32,256 | allure-framework/allure-java | allure-java-commons/src/main/java/io/qameta/allure/AllureLifecycle.java | AllureLifecycle.startStep | public void startStep(final String parentUuid, final String uuid, final StepResult result) {
notifier.beforeStepStart(result);
result.setStage(Stage.RUNNING);
result.setStart(System.currentTimeMillis());
threadContext.start(uuid);
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synchronized (storage) {
parentStep.getSteps().add(result);
}
});
notifier.afterStepStart(result);
} | java | public void startStep(final String parentUuid, final String uuid, final StepResult result) {
notifier.beforeStepStart(result);
result.setStage(Stage.RUNNING);
result.setStart(System.currentTimeMillis());
threadContext.start(uuid);
storage.put(uuid, result);
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32,257 | allure-framework/allure-java | allure-java-commons/src/main/java/io/qameta/allure/AllureLifecycle.java | AllureLifecycle.updateStep | public void updateStep(final String uuid, final Consumer<StepResult> update) {
final Optional<StepResult> found = storage.getStep(uuid);
if (!found.isPresent()) {
LOGGER.error("Could not update step: step with uuid {} not found", uuid);
return;
}
final StepResult step = found.get();
notifier.beforeStepUpdate(step);
update.accept(step);
notifier.afterStepUpdate(step);
} | java | public void updateStep(final String uuid, final Consumer<StepResult> update) {
final Optional<StepResult> found = storage.getStep(uuid);
if (!found.isPresent()) {
LOGGER.error("Could not update step: step with uuid {} not found", uuid);
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32,258 | allure-framework/allure-java | allure-java-commons/src/main/java/io/qameta/allure/AllureLifecycle.java | AllureLifecycle.stopStep | public void stopStep(final String uuid) {
final Optional<StepResult> found = storage.getStep(uuid);
if (!found.isPresent()) {
LOGGER.error("Could not stop step: step with uuid {} not found", uuid);
return;
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notifier.beforeStepStop(step);
step.setStage(Stage.FINISHED);
step.setStop(System.currentTimeMillis());
storage.remove(uuid);
threadContext.stop();
notifier.afterStepStop(step);
} | java | public void stopStep(final String uuid) {
final Optional<StepResult> found = storage.getStep(uuid);
if (!found.isPresent()) {
LOGGER.error("Could not stop step: step with uuid {} not found", uuid);
return;
}
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32,259 | allure-framework/allure-java | allure-java-commons/src/main/java/io/qameta/allure/AllureLifecycle.java | AllureLifecycle.addAttachment | public void addAttachment(final String name, final String type,
final String fileExtension, final InputStream stream) {
writeAttachment(prepareAttachment(name, type, fileExtension), stream);
} | java | public void addAttachment(final String name, final String type,
final String fileExtension, final InputStream stream) {
writeAttachment(prepareAttachment(name, type, fileExtension), stream);
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32,260 | allure-framework/allure-java | allure-java-commons/src/main/java/io/qameta/allure/util/AnnotationUtils.java | AnnotationUtils.getLinks | public static List<Link> getLinks(final AnnotatedElement annotatedElement) {
final List<Link> result = new ArrayList<>();
result.addAll(extractLinks(annotatedElement, io.qameta.allure.Link.class, ResultsUtils::createLink));
result.addAll(extractLinks(annotatedElement, io.qameta.allure.Issue.class, ResultsUtils::createLink));
result.addAll(extractLinks(annotatedElement, io.qameta.allure.TmsLink.class, ResultsUtils::createLink));
return result;
} | java | public static List<Link> getLinks(final AnnotatedElement annotatedElement) {
final List<Link> result = new ArrayList<>();
result.addAll(extractLinks(annotatedElement, io.qameta.allure.Link.class, ResultsUtils::createLink));
result.addAll(extractLinks(annotatedElement, io.qameta.allure.Issue.class, ResultsUtils::createLink));
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return result;
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32,261 | allure-framework/allure-java | allure-java-commons/src/main/java/io/qameta/allure/util/AnnotationUtils.java | AnnotationUtils.getLinks | public static List<Link> getLinks(final Collection<Annotation> annotations) {
final List<Link> result = new ArrayList<>();
result.addAll(extractLinks(annotations, io.qameta.allure.Link.class, ResultsUtils::createLink));
result.addAll(extractLinks(annotations, io.qameta.allure.Issue.class, ResultsUtils::createLink));
result.addAll(extractLinks(annotations, io.qameta.allure.TmsLink.class, ResultsUtils::createLink));
return result;
} | java | public static List<Link> getLinks(final Collection<Annotation> annotations) {
final List<Link> result = new ArrayList<>();
result.addAll(extractLinks(annotations, io.qameta.allure.Link.class, ResultsUtils::createLink));
result.addAll(extractLinks(annotations, io.qameta.allure.Issue.class, ResultsUtils::createLink));
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32,262 | allure-framework/allure-java | allure-java-commons/src/main/java/io/qameta/allure/util/AnnotationUtils.java | AnnotationUtils.getLabels | public static Set<Label> getLabels(final Collection<Annotation> annotations) {
return annotations.stream()
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.map(AnnotationUtils::getMarks)
.flatMap(Collection::stream)
.collect(Collectors.toSet());
} | java | public static Set<Label> getLabels(final Collection<Annotation> annotations) {
return annotations.stream()
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.flatMap(Collection::stream)
.collect(Collectors.toSet());
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32,263 | jenkinsci/java-client-api | jenkins-client/src/main/java/com/offbytwo/jenkins/JenkinsServer.java | JenkinsServer.isRunning | public boolean isRunning() {
try {
client.get("/");
return true;
} catch (IOException e) {
LOGGER.debug("isRunning()", e);
return false;
}
} | java | public boolean isRunning() {
try {
client.get("/");
return true;
} catch (IOException e) {
LOGGER.debug("isRunning()", e);
return false;
}
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32,264 | jenkinsci/java-client-api | jenkins-client/src/main/java/com/offbytwo/jenkins/JenkinsServer.java | JenkinsServer.getView | public View getView(FolderJob folder, String name) throws IOException {
try {
View resultView = client.get(UrlUtils.toViewBaseUrl(folder, name) + "/", View.class);
resultView.setClient(client);
// TODO: Think about the following? Does there exists a simpler/more
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for (Job job : resultView.getJobs()) {
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for (View view : resultView.getViews()) {
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if (e.getStatusCode() == HttpStatus.SC_NOT_FOUND) {
// TODO: Think hard about this.
return null;
}
throw e;
}
} | java | public View getView(FolderJob folder, String name) throws IOException {
try {
View resultView = client.get(UrlUtils.toViewBaseUrl(folder, name) + "/", View.class);
resultView.setClient(client);
// TODO: Think about the following? Does there exists a simpler/more
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for (Job job : resultView.getJobs()) {
job.setClient(client);
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view.setClient(client);
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return resultView;
} catch (HttpResponseException e) {
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32,265 | jenkinsci/java-client-api | jenkins-client/src/main/java/com/offbytwo/jenkins/JenkinsServer.java | JenkinsServer.getJob | public JobWithDetails getJob(String jobName) throws IOException {
return getJob(null, UrlUtils.toFullJobPath(jobName));
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32,266 | jenkinsci/java-client-api | jenkins-client/src/main/java/com/offbytwo/jenkins/JenkinsServer.java | JenkinsServer.getJob | public JobWithDetails getJob(FolderJob folder, String jobName) throws IOException {
try {
JobWithDetails job = client.get(UrlUtils.toJobBaseUrl(folder, jobName), JobWithDetails.class);
job.setClient(client);
return job;
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if (e.getStatusCode() == HttpStatus.SC_NOT_FOUND) {
// TODO: Think hard about this.
return null;
}
throw e;
}
} | java | public JobWithDetails getJob(FolderJob folder, String jobName) throws IOException {
try {
JobWithDetails job = client.get(UrlUtils.toJobBaseUrl(folder, jobName), JobWithDetails.class);
job.setClient(client);
return job;
} catch (HttpResponseException e) {
LOGGER.debug("getJob(folder={}, jobName={}) status={}", folder, jobName, e.getStatusCode());
if (e.getStatusCode() == HttpStatus.SC_NOT_FOUND) {
// TODO: Think hard about this.
return null;
}
throw e;
}
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32,267 | jenkinsci/java-client-api | jenkins-client/src/main/java/com/offbytwo/jenkins/JenkinsServer.java | JenkinsServer.createView | public JenkinsServer createView(String viewName, String viewXml) throws IOException {
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32,268 | jenkinsci/java-client-api | jenkins-client/src/main/java/com/offbytwo/jenkins/JenkinsServer.java | JenkinsServer.createView | public JenkinsServer createView(String viewName, String viewXml, Boolean crumbFlag) throws IOException {
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32,269 | jenkinsci/java-client-api | jenkins-client/src/main/java/com/offbytwo/jenkins/JenkinsServer.java | JenkinsServer.getJobXml | public String getJobXml(FolderJob folder, String jobName) throws IOException {
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32,270 | jenkinsci/java-client-api | jenkins-client/src/main/java/com/offbytwo/jenkins/JenkinsServer.java | JenkinsServer.getLabel | public LabelWithDetails getLabel(String labelName) throws IOException {
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} | java | public LabelWithDetails getLabel(String labelName) throws IOException {
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32,271 | jenkinsci/java-client-api | jenkins-client/src/main/java/com/offbytwo/jenkins/JenkinsServer.java | JenkinsServer.updateView | public JenkinsServer updateView(String viewName, String viewXml) throws IOException {
return this.updateView(viewName, viewXml, true);
} | java | public JenkinsServer updateView(String viewName, String viewXml) throws IOException {
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32,272 | jenkinsci/java-client-api | jenkins-client/src/main/java/com/offbytwo/jenkins/JenkinsServer.java | JenkinsServer.enableJob | public JenkinsServer enableJob(String jobName, boolean crumbFlag) throws IOException {
client.post("/job/" + EncodingUtils.encode(jobName) + "/enable", crumbFlag);
return this;
} | java | public JenkinsServer enableJob(String jobName, boolean crumbFlag) throws IOException {
client.post("/job/" + EncodingUtils.encode(jobName) + "/enable", crumbFlag);
return this;
} | [
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32,273 | jenkinsci/java-client-api | jenkins-client/src/main/java/com/offbytwo/jenkins/JenkinsServer.java | JenkinsServer.runScript | public String runScript(String script, boolean crumbFlag) throws IOException {
return client.post_text("/scriptText", "script=" + script, ContentType.APPLICATION_FORM_URLENCODED, crumbFlag);
} | java | public String runScript(String script, boolean crumbFlag) throws IOException {
return client.post_text("/scriptText", "script=" + script, ContentType.APPLICATION_FORM_URLENCODED, crumbFlag);
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32,274 | jenkinsci/java-client-api | jenkins-client/src/main/java/com/offbytwo/jenkins/JenkinsServer.java | JenkinsServer.restart | public JenkinsServer restart(Boolean crumbFlag) throws IOException {
try {
client.post("/restart", crumbFlag);
} catch (org.apache.http.client.ClientProtocolException e) {
LOGGER.error("restart()", e);
}
return this;
} | java | public JenkinsServer restart(Boolean crumbFlag) throws IOException {
try {
client.post("/restart", crumbFlag);
} catch (org.apache.http.client.ClientProtocolException e) {
LOGGER.error("restart()", e);
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32,275 | jenkinsci/java-client-api | jenkins-client/src/main/java/com/offbytwo/jenkins/client/JenkinsHttpClient.java | JenkinsHttpClient.addAuthentication | protected static HttpClientBuilder addAuthentication(final HttpClientBuilder builder,
final URI uri, final String username,
String password) {
if (isNotBlank(username)) {
CredentialsProvider provider = new BasicCredentialsProvider();
AuthScope scope = new AuthScope(uri.getHost(), uri.getPort(), "realm");
UsernamePasswordCredentials credentials = new UsernamePasswordCredentials(username, password);
provider.setCredentials(scope, credentials);
builder.setDefaultCredentialsProvider(provider);
builder.addInterceptorFirst(new PreemptiveAuth());
}
return builder;
} | java | protected static HttpClientBuilder addAuthentication(final HttpClientBuilder builder,
final URI uri, final String username,
String password) {
if (isNotBlank(username)) {
CredentialsProvider provider = new BasicCredentialsProvider();
AuthScope scope = new AuthScope(uri.getHost(), uri.getPort(), "realm");
UsernamePasswordCredentials credentials = new UsernamePasswordCredentials(username, password);
provider.setCredentials(scope, credentials);
builder.setDefaultCredentialsProvider(provider);
builder.addInterceptorFirst(new PreemptiveAuth());
}
return builder;
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32,276 | jenkinsci/java-client-api | jenkins-client/src/main/java/com/offbytwo/jenkins/client/util/ResponseUtils.java | ResponseUtils.getJenkinsVersion | public static String getJenkinsVersion(final HttpResponse response) {
final Header[] hdrs = response.getHeaders("X-Jenkins");
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} | java | public static String getJenkinsVersion(final HttpResponse response) {
final Header[] hdrs = response.getHeaders("X-Jenkins");
return hdrs.length == 0 ? "" : hdrs[0].getValue();
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32,277 | jenkinsci/java-client-api | jenkins-client/src/main/java/com/offbytwo/jenkins/model/JobWithDetails.java | JobWithDetails.getBuildByNumber | public Optional<Build> getBuildByNumber(final int buildNumber) {
return builds.stream().filter(isBuildNumberEqualTo(buildNumber)).findFirst();
} | java | public Optional<Build> getBuildByNumber(final int buildNumber) {
return builds.stream().filter(isBuildNumberEqualTo(buildNumber)).findFirst();
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32,278 | jenkinsci/java-client-api | jenkins-client/src/main/java/com/offbytwo/jenkins/client/util/UrlUtils.java | UrlUtils.toJobBaseUrl | public static String toJobBaseUrl(final FolderJob folder, final String jobName) {
final StringBuilder sb = new StringBuilder(DEFAULT_BUFFER_SIZE);
sb.append(UrlUtils.toBaseUrl(folder));
if (sb.charAt(sb.length() - 1) != '/') sb.append('/');
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sb.append(EncodingUtils.encode(jobNameParts[i]));
if (i != jobNameParts.length - 1) sb.append('/');
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return sb.toString();
} | java | public static String toJobBaseUrl(final FolderJob folder, final String jobName) {
final StringBuilder sb = new StringBuilder(DEFAULT_BUFFER_SIZE);
sb.append(UrlUtils.toBaseUrl(folder));
if (sb.charAt(sb.length() - 1) != '/') sb.append('/');
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32,279 | jenkinsci/java-client-api | jenkins-client/src/main/java/com/offbytwo/jenkins/client/util/UrlUtils.java | UrlUtils.toViewBaseUrl | public static String toViewBaseUrl(final FolderJob folder, final String name) {
final StringBuilder sb = new StringBuilder(DEFAULT_BUFFER_SIZE);
final String base = UrlUtils.toBaseUrl(folder);
sb.append(base);
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} | java | public static String toViewBaseUrl(final FolderJob folder, final String name) {
final StringBuilder sb = new StringBuilder(DEFAULT_BUFFER_SIZE);
final String base = UrlUtils.toBaseUrl(folder);
sb.append(base);
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32,280 | jenkinsci/java-client-api | jenkins-client/src/main/java/com/offbytwo/jenkins/client/util/UrlUtils.java | UrlUtils.toFullJobPath | public static String toFullJobPath(final String jobName) {
final String[] parts = jobName.split("/");
if (parts.length == 1) return parts[0];
final StringBuilder sb = new StringBuilder(DEFAULT_BUFFER_SIZE);
for (int i = 0; i < parts.length; i++) {
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} | java | public static String toFullJobPath(final String jobName) {
final String[] parts = jobName.split("/");
if (parts.length == 1) return parts[0];
final StringBuilder sb = new StringBuilder(DEFAULT_BUFFER_SIZE);
for (int i = 0; i < parts.length; i++) {
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32,281 | jenkinsci/java-client-api | jenkins-client/src/main/java/com/offbytwo/jenkins/client/util/UrlUtils.java | UrlUtils.toJsonApiUri | public static URI toJsonApiUri(final URI uri, final String context, final String path) {
String p = path;
if (!p.matches("(?i)https?://.*")) p = join(context, p);
if (!p.contains("?")) {
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final String[] components = p.split("\\?", 2);
p = join(components[0], "api/json") + "?" + components[1];
}
return uri.resolve("/").resolve(p.replace(" ", "%20"));
} | java | public static URI toJsonApiUri(final URI uri, final String context, final String path) {
String p = path;
if (!p.matches("(?i)https?://.*")) p = join(context, p);
if (!p.contains("?")) {
p = join(p, "api/json");
} else {
final String[] components = p.split("\\?", 2);
p = join(components[0], "api/json") + "?" + components[1];
}
return uri.resolve("/").resolve(p.replace(" ", "%20"));
} | [
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32,282 | jenkinsci/java-client-api | jenkins-client/src/main/java/com/offbytwo/jenkins/client/util/UrlUtils.java | UrlUtils.toNoApiUri | public static URI toNoApiUri(final URI uri, final String context, final String path) {
final String p = path.matches("(?i)https?://.*") ? path : join(context, path);
return uri.resolve("/").resolve(p);
} | java | public static URI toNoApiUri(final URI uri, final String context, final String path) {
final String p = path.matches("(?i)https?://.*") ? path : join(context, path);
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32,283 | jenkinsci/java-client-api | jenkins-client/src/main/java/com/offbytwo/jenkins/model/Job.java | Job.getFileFromWorkspace | public String getFileFromWorkspace(String fileName) throws IOException {
InputStream is = client.getFile(URI.create(url + "/ws/" + fileName));
ByteArrayOutputStream result = new ByteArrayOutputStream();
byte[] buffer = new byte[1024];
int length;
while ((length = is.read(buffer)) != -1) {
result.write(buffer, 0, length);
}
return result.toString("UTF-8");
} | java | public String getFileFromWorkspace(String fileName) throws IOException {
InputStream is = client.getFile(URI.create(url + "/ws/" + fileName));
ByteArrayOutputStream result = new ByteArrayOutputStream();
byte[] buffer = new byte[1024];
int length;
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32,284 | jenkinsci/java-client-api | jenkins-client/src/main/java/com/offbytwo/jenkins/model/Job.java | Job.build | public QueueReference build() throws IOException {
ExtractHeader location = client.post(url + "build", null, ExtractHeader.class, false);
return new QueueReference(location.getLocation());
} | java | public QueueReference build() throws IOException {
ExtractHeader location = client.post(url + "build", null, ExtractHeader.class, false);
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32,285 | jenkinsci/java-client-api | jenkins-client/src/main/java/com/offbytwo/jenkins/model/Job.java | Job.build | public QueueReference build(Map<String, String> params, Map<String, File> fileParams) throws IOException {
return build(params,fileParams,false);
} | java | public QueueReference build(Map<String, String> params, Map<String, File> fileParams) throws IOException {
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32,286 | jenkinsci/java-client-api | jenkins-client/src/main/java/com/offbytwo/jenkins/model/Job.java | Job.build | public QueueReference build(Map<String, String> params, Map<String, File> fileParams, boolean crumbFlag) throws IOException {
String qs = params.entrySet().stream()
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ExtractHeader location = client.post(url + "buildWithParameters?" + qs,null, ExtractHeader.class, fileParams, crumbFlag);
return new QueueReference(location.getLocation());
} | java | public QueueReference build(Map<String, String> params, Map<String, File> fileParams, boolean crumbFlag) throws IOException {
String qs = params.entrySet().stream()
.map(s -> s.getKey() + "=" + s.getValue())
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// String qs = join(Collections2.transform(params.entrySet(), new MapEntryToQueryStringPair()), "&");
ExtractHeader location = client.post(url + "buildWithParameters?" + qs,null, ExtractHeader.class, fileParams, crumbFlag);
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32,287 | jenkinsci/java-client-api | jenkins-client/src/main/java/com/offbytwo/jenkins/helper/ComparableVersion.java | ComparableVersion.main | public static void main( String... args )
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if ( args.length == 0 )
{
return;
}
ComparableVersion prev = null;
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ComparableVersion c = new ComparableVersion( version );
if ( prev != null )
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int compare = prev.compareTo( c );
System.out.println( " " + prev.toString() + ' '
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}
System.out.println( String.valueOf( i++ ) + ". " + version + " == " + c.getCanonical() );
prev = c;
}
} | java | public static void main( String... args )
{
System.out.println( "Display parameters as parsed by Maven (in canonical form) and comparison result:" );
if ( args.length == 0 )
{
return;
}
ComparableVersion prev = null;
int i = 1;
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{
ComparableVersion c = new ComparableVersion( version );
if ( prev != null )
{
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}
System.out.println( String.valueOf( i++ ) + ". " + version + " == " + c.getCanonical() );
prev = c;
}
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32,288 | jenkinsci/java-client-api | jenkins-client/src/main/java/com/offbytwo/jenkins/model/FolderJob.java | FolderJob.getJobs | public Map<String, Job> getJobs() {
//FIXME: Check for null of jobs? Can that happen?
return jobs.stream()
.map(SET_CLIENT(this.client))
.collect(Collectors.toMap(k -> k.getName(), Function.identity()));
} | java | public Map<String, Job> getJobs() {
//FIXME: Check for null of jobs? Can that happen?
return jobs.stream()
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.collect(Collectors.toMap(k -> k.getName(), Function.identity()));
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32,289 | jenkinsci/java-client-api | jenkins-client/src/main/java/com/offbytwo/jenkins/model/FolderJob.java | FolderJob.getJob | public Job getJob(String name) {
//FIXME: Check for null of jobs? Can that happen?
return jobs.stream()
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} | java | public Job getJob(String name) {
//FIXME: Check for null of jobs? Can that happen?
return jobs.stream()
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32,290 | jenkinsci/java-client-api | jenkins-client/src/main/java/com/offbytwo/jenkins/model/BuildWithDetails.java | BuildWithDetails.streamConsoleOutput | public void streamConsoleOutput(final BuildConsoleStreamListener listener, final int poolingInterval, final int poolingTimeout, boolean crumbFlag) throws InterruptedException, IOException {
// Calculate start and timeout
final long startTime = System.currentTimeMillis();
final long timeoutTime = startTime + (poolingTimeout * 1000);
int bufferOffset = 0;
while (true) {
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String logString = consoleLog.getConsoleLog();
if (logString != null && !logString.isEmpty()) {
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if (consoleLog.getHasMoreData()) {
bufferOffset = consoleLog.getCurrentBufferSize();
} else {
listener.finished();
break;
}
long currentTime = System.currentTimeMillis();
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break;
}
}
} | java | public void streamConsoleOutput(final BuildConsoleStreamListener listener, final int poolingInterval, final int poolingTimeout, boolean crumbFlag) throws InterruptedException, IOException {
// Calculate start and timeout
final long startTime = System.currentTimeMillis();
final long timeoutTime = startTime + (poolingTimeout * 1000);
int bufferOffset = 0;
while (true) {
Thread.sleep(poolingInterval * 1000);
ConsoleLog consoleLog = null;
consoleLog = getConsoleOutputText(bufferOffset, crumbFlag);
String logString = consoleLog.getConsoleLog();
if (logString != null && !logString.isEmpty()) {
listener.onData(logString);
}
if (consoleLog.getHasMoreData()) {
bufferOffset = consoleLog.getCurrentBufferSize();
} else {
listener.finished();
break;
}
long currentTime = System.currentTimeMillis();
if (currentTime > timeoutTime) {
LOGGER.warn("Pooling for build {0} for {2} timeout! Check if job stuck in jenkins",
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break;
}
}
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32,291 | jenkinsci/java-client-api | jenkins-client/src/main/java/com/offbytwo/jenkins/model/BuildWithDetails.java | BuildWithDetails.getConsoleOutputText | public ConsoleLog getConsoleOutputText(int bufferOffset, boolean crumbFlag) throws IOException {
List<NameValuePair> formData = new ArrayList<>();
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}
return new ConsoleLog(response, hasMoreData, currentBufferSize);
} | java | public ConsoleLog getConsoleOutputText(int bufferOffset, boolean crumbFlag) throws IOException {
List<NameValuePair> formData = new ArrayList<>();
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String path = getUrl() + "logText/progressiveText";
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boolean hasMoreData = false;
if (moreDataHeader != null) {
hasMoreData = Boolean.TRUE.toString().equals(moreDataHeader.getValue());
}
Integer currentBufferSize = bufferOffset;
if (textSizeHeader != null) {
try {
currentBufferSize = Integer.parseInt(textSizeHeader.getValue());
} catch (NumberFormatException e) {
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return new ConsoleLog(response, hasMoreData, currentBufferSize);
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] | c4f5953d3d4dda92cd946ad3bf2b811524c32da9 | https://github.com/jenkinsci/java-client-api/blob/c4f5953d3d4dda92cd946ad3bf2b811524c32da9/jenkins-client/src/main/java/com/offbytwo/jenkins/model/BuildWithDetails.java#L436-L458 |
32,292 | jenkinsci/java-client-api | jenkins-client/src/main/java/com/offbytwo/jenkins/model/BuildWithDetails.java | BuildWithDetails.getChangeSet | public BuildChangeSet getChangeSet() {
BuildChangeSet result;
if (changeSet != null) {
result = changeSet;
} else if (changeSets != null && !changeSets.isEmpty()) {
result = changeSets.get(0);
} else {
result = null;
}
return result;
} | java | public BuildChangeSet getChangeSet() {
BuildChangeSet result;
if (changeSet != null) {
result = changeSet;
} else if (changeSets != null && !changeSets.isEmpty()) {
result = changeSets.get(0);
} else {
result = null;
}
return result;
} | [
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If a build performs several scm checkouts (i.e. pipeline builds), the change set of the first
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If no checkout is performed, null is returned.
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32,293 | jenkinsci/java-client-api | jenkins-client/src/main/java/com/offbytwo/jenkins/model/BuildWithDetails.java | BuildWithDetails.getChangeSets | public List<BuildChangeSet> getChangeSets() {
List<BuildChangeSet> result;
if (changeSets != null) {
result = changeSets;
} else if (changeSet != null) {
result = Collections.singletonList(changeSet);
} else {
result = null;
}
return result;
} | java | public List<BuildChangeSet> getChangeSets() {
List<BuildChangeSet> result;
if (changeSets != null) {
result = changeSets;
} else if (changeSet != null) {
result = Collections.singletonList(changeSet);
} else {
result = null;
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32,294 | jenkinsci/java-client-api | jenkins-client/src/main/java/com/offbytwo/jenkins/model/Build.java | Build.Stop | public String Stop(boolean crumbFlag) throws HttpResponseException, IOException {
try {
return client.get(url + "stop");
} catch (HttpResponseException ex) {
if (ex.getStatusCode() == HttpStatus.SC_METHOD_NOT_ALLOWED) {
stopPost(crumbFlag);
return "";
}
throw ex;
}
} | java | public String Stop(boolean crumbFlag) throws HttpResponseException, IOException {
try {
return client.get(url + "stop");
} catch (HttpResponseException ex) {
if (ex.getStatusCode() == HttpStatus.SC_METHOD_NOT_ALLOWED) {
stopPost(crumbFlag);
return "";
}
throw ex;
}
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@param crumbFlag flag used to specify if a crumb is passed into for the request
@return the client url
@throws HttpResponseException in case of an error.
@throws IOException in case of an error. | [
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32,295 | Tourenathan-G5organisation/SiliCompressor | silicompressor/src/main/java/com/iceteck/silicompressorr/FileUtils.java | FileUtils.getExtension | public static String getExtension(String uri) {
if (uri == null) {
return null;
}
int dot = uri.lastIndexOf(".");
if (dot >= 0) {
return uri.substring(dot);
} else {
// No extension.
return "";
}
} | java | public static String getExtension(String uri) {
if (uri == null) {
return null;
}
int dot = uri.lastIndexOf(".");
if (dot >= 0) {
return uri.substring(dot);
} else {
// No extension.
return "";
}
} | [
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@param uri
@return Extension including the dot("."); "" if there is no extension;
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32,296 | Tourenathan-G5organisation/SiliCompressor | silicompressor/src/main/java/com/iceteck/silicompressorr/FileUtils.java | FileUtils.getUri | public static Uri getUri(Context context, File file) {
if (file != null) {
return FileProvider.getUriForFile(context, FILE_PROVIDER_AUTHORITY, file);
//Uri.fromFile(file);
}
return null;
} | java | public static Uri getUri(Context context, File file) {
if (file != null) {
return FileProvider.getUriForFile(context, FILE_PROVIDER_AUTHORITY, file);
//Uri.fromFile(file);
}
return null;
} | [
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@param file
@return uri | [
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] | 546f6cd7b2a7a783e1122df46c1e237f8938fe72 | https://github.com/Tourenathan-G5organisation/SiliCompressor/blob/546f6cd7b2a7a783e1122df46c1e237f8938fe72/silicompressor/src/main/java/com/iceteck/silicompressorr/FileUtils.java#L109-L115 |
32,297 | Tourenathan-G5organisation/SiliCompressor | silicompressor/src/main/java/com/iceteck/silicompressorr/FileUtils.java | FileUtils.getFile | public static File getFile(Context context, Uri uri) {
if (uri != null) {
String path = getPath(context, uri);
if (path != null && isLocal(path)) {
return new File(path);
}
}
return null;
} | java | public static File getFile(Context context, Uri uri) {
if (uri != null) {
String path = getPath(context, uri);
if (path != null && isLocal(path)) {
return new File(path);
}
}
return null;
} | [
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@return file A local file that the Uri was pointing to, or null if the
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@author paulburke | [
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] | 546f6cd7b2a7a783e1122df46c1e237f8938fe72 | https://github.com/Tourenathan-G5organisation/SiliCompressor/blob/546f6cd7b2a7a783e1122df46c1e237f8938fe72/silicompressor/src/main/java/com/iceteck/silicompressorr/FileUtils.java#L342-L350 |
32,298 | Tourenathan-G5organisation/SiliCompressor | silicompressor/src/main/java/com/iceteck/silicompressorr/FileUtils.java | FileUtils.getReadableFileSize | public static String getReadableFileSize(int size) {
final int BYTES_IN_KILOBYTES = 1024;
final DecimalFormat dec = new DecimalFormat("###.#");
final String KILOBYTES = " KB";
final String MEGABYTES = " MB";
final String GIGABYTES = " GB";
float fileSize = 0;
String suffix = KILOBYTES;
if (size > BYTES_IN_KILOBYTES) {
fileSize = size / BYTES_IN_KILOBYTES;
if (fileSize > BYTES_IN_KILOBYTES) {
fileSize = fileSize / BYTES_IN_KILOBYTES;
if (fileSize > BYTES_IN_KILOBYTES) {
fileSize = fileSize / BYTES_IN_KILOBYTES;
suffix = GIGABYTES;
} else {
suffix = MEGABYTES;
}
}
}
return String.valueOf(dec.format(fileSize) + suffix);
} | java | public static String getReadableFileSize(int size) {
final int BYTES_IN_KILOBYTES = 1024;
final DecimalFormat dec = new DecimalFormat("###.#");
final String KILOBYTES = " KB";
final String MEGABYTES = " MB";
final String GIGABYTES = " GB";
float fileSize = 0;
String suffix = KILOBYTES;
if (size > BYTES_IN_KILOBYTES) {
fileSize = size / BYTES_IN_KILOBYTES;
if (fileSize > BYTES_IN_KILOBYTES) {
fileSize = fileSize / BYTES_IN_KILOBYTES;
if (fileSize > BYTES_IN_KILOBYTES) {
fileSize = fileSize / BYTES_IN_KILOBYTES;
suffix = GIGABYTES;
} else {
suffix = MEGABYTES;
}
}
}
return String.valueOf(dec.format(fileSize) + suffix);
} | [
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... | Get the file size in a human-readable string.
@param size
@return
@author paulburke | [
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] | 546f6cd7b2a7a783e1122df46c1e237f8938fe72 | https://github.com/Tourenathan-G5organisation/SiliCompressor/blob/546f6cd7b2a7a783e1122df46c1e237f8938fe72/silicompressor/src/main/java/com/iceteck/silicompressorr/FileUtils.java#L359-L381 |
32,299 | Tourenathan-G5organisation/SiliCompressor | silicompressor/src/main/java/com/iceteck/silicompressorr/FileUtils.java | FileUtils.getThumbnail | public static Bitmap getThumbnail(Context context, File file) {
return getThumbnail(context, getUri(context, file), getMimeType(file));
} | java | public static Bitmap getThumbnail(Context context, File file) {
return getThumbnail(context, getUri(context, file), getMimeType(file));
} | [
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] | Attempt to retrieve the thumbnail of given File from the MediaStore. This
should not be called on the UI thread.
@param context
@param file
@return
@author paulburke | [
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