import java.util.List;
import java.util.Vector;
-public class AppletPDBCanvas extends Panel implements MouseListener,
- MouseMotionListener, StructureListener
+public class AppletPDBCanvas extends Panel
+ implements MouseListener, MouseMotionListener, StructureListener
{
MCMatrix idmat = new MCMatrix(3, 3);
for (int i = 0; i < pdb.getChains().size(); i++)
{
- mappingDetails
- .append("\n\nPDB Sequence is :\nSequence = "
- + pdb.getChains().elementAt(i).sequence
- .getSequenceAsString());
+ mappingDetails.append("\n\nPDB Sequence is :\nSequence = "
+ + pdb.getChains().elementAt(i).sequence
+ .getSequenceAsString());
mappingDetails.append("\nNo of residues = "
+ pdb.getChains().elementAt(i).residues.size() + "\n\n");
// Align the sequence to the pdb
// TODO: DNa/Pep switch
AlignSeq as = new AlignSeq(sequence,
- pdb.getChains().elementAt(i).sequence, pdb.getChains()
- .elementAt(i).isNa ? AlignSeq.DNA : AlignSeq.PEP);
+ pdb.getChains().elementAt(i).sequence,
+ pdb.getChains().elementAt(i).isNa ? AlignSeq.DNA
+ : AlignSeq.PEP);
as.calcScoreMatrix();
as.traceAlignment();
PrintStream ps = new PrintStream(System.out)
g.fillRect(0, 0, getSize().width, getSize().height);
g.setColor(Color.black);
g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString(
- MessageManager.getString("label.error_loading_pdb_data"), 50,
- getSize().height / 2);
+ g.drawString(MessageManager.getString("label.error_loading_pdb_data"),
+ 50, getSize().height / 2);
return;
}
if (pos > 0)
{
pos = sequence[s].findIndex(pos);
- tmp.endCol = sr
- .getResidueColour(sequence[s], pos, finder);
+ tmp.endCol = sr.getResidueColour(sequence[s], pos,
+ finder);
}
}
}
{
tmpBond = visiblebonds.elementAt(i);
- xstart = (int) (((tmpBond.start[0] - centre[0]) * scale) + (getSize().width / 2));
- ystart = (int) (((centre[1] - tmpBond.start[1]) * scale) + (getSize().height / 2));
+ xstart = (int) (((tmpBond.start[0] - centre[0]) * scale)
+ + (getSize().width / 2));
+ ystart = (int) (((centre[1] - tmpBond.start[1]) * scale)
+ + (getSize().height / 2));
- xend = (int) (((tmpBond.end[0] - centre[0]) * scale) + (getSize().width / 2));
- yend = (int) (((centre[1] - tmpBond.end[1]) * scale) + (getSize().height / 2));
+ xend = (int) (((tmpBond.end[0] - centre[0]) * scale)
+ + (getSize().width / 2));
+ yend = (int) (((centre[1] - tmpBond.end[1]) * scale)
+ + (getSize().height / 2));
xmid = (xend + xstart) / 2;
ymid = (yend + ystart) / 2;
if (n == 1)
{
- int xstart = (int) (((b.start[0] - centre[0]) * scale) + (getSize().width / 2));
- int ystart = (int) (((centre[1] - b.start[1]) * scale) + (getSize().height / 2));
+ int xstart = (int) (((b.start[0] - centre[0]) * scale)
+ + (getSize().width / 2));
+ int ystart = (int) (((centre[1] - b.start[1]) * scale)
+ + (getSize().height / 2));
g.setColor(Color.red);
g.drawString(b.at1.resName + "-" + b.at1.resNumber, xstart, ystart);
if (n == 2)
{
- int xstart = (int) (((b.end[0] - centre[0]) * scale) + (getSize().width / 2));
- int ystart = (int) (((centre[1] - b.end[1]) * scale) + (getSize().height / 2));
+ int xstart = (int) (((b.end[0] - centre[0]) * scale)
+ + (getSize().width / 2));
+ int ystart = (int) (((centre[1] - b.end[1]) * scale)
+ + (getSize().height / 2));
g.setColor(Color.red);
g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart);
{
tmpBond = bonds.elementAt(i);
- truex = (int) (((tmpBond.start[0] - centre[0]) * scale) + (getSize().width / 2));
+ truex = (int) (((tmpBond.start[0] - centre[0]) * scale)
+ + (getSize().width / 2));
if (Math.abs(truex - x) <= 2)
{
- int truey = (int) (((centre[1] - tmpBond.start[1]) * scale) + (getSize().height / 2));
+ int truey = (int) (((centre[1] - tmpBond.start[1]) * scale)
+ + (getSize().height / 2));
if (Math.abs(truey - y) <= 2)
{
// Still here? Maybe its the last bond
- truex = (int) (((tmpBond.end[0] - centre[0]) * scale) + (getSize().width / 2));
+ truex = (int) (((tmpBond.end[0] - centre[0]) * scale)
+ + (getSize().width / 2));
if (Math.abs(truex - x) <= 2)
{
- int truey = (int) (((tmpBond.end[1] - centre[1]) * scale) + (getSize().height / 2));
+ int truey = (int) (((tmpBond.end[1] - centre[1]) * scale)
+ + (getSize().height / 2));
if (Math.abs(truey - y) <= 2)
{
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
-public class AppletPDBViewer extends EmbmenuFrame implements
- ActionListener, ItemListener
+public class AppletPDBViewer extends EmbmenuFrame
+ implements ActionListener, ItemListener
{
AppletPDBCanvas pdbcanvas;
embedMenuIfNeeded(pdbcanvas);
add(pdbcanvas, BorderLayout.CENTER);
- StringBuffer title = new StringBuffer(seq[0].getName() + ":"
- + pdbcanvas.pdbentry.getFile());
+ StringBuffer title = new StringBuffer(
+ seq[0].getName() + ":" + pdbcanvas.pdbentry.getFile());
jalview.bin.JalviewLite.addFrame(this, title.toString(), 400, 400);
zbuffer.addItemListener(this);
charge.setLabel(MessageManager.getString("label.charge_cysteine"));
charge.addActionListener(this);
- hydro.setLabel(MessageManager
- .getString("label.colourScheme_hydrophobic"));
+ hydro.setLabel(
+ MessageManager.getString("label.colourScheme_hydrophobic"));
hydro.addActionListener(this);
chain.setLabel(MessageManager.getString("action.by_chain"));
chain.addActionListener(this);
strand.setLabel(MessageManager
.getString("label.colourScheme_strand_propensity"));
strand.addActionListener(this);
- turn.setLabel(MessageManager
- .getString("label.colourScheme_turn_propensity"));
+ turn.setLabel(
+ MessageManager.getString("label.colourScheme_turn_propensity"));
turn.addActionListener(this);
- buried.setLabel(MessageManager
- .getString("label.colourScheme_buried_index"));
+ buried.setLabel(
+ MessageManager.getString("label.colourScheme_buried_index"));
buried.addActionListener(this);
user.setLabel(MessageManager.getString("action.user_defined"));
user.addActionListener(this);
import javax.swing.JPanel;
import javax.swing.ToolTipManager;
-public class PDBCanvas extends JPanel implements MouseListener,
- MouseMotionListener, StructureListener
+public class PDBCanvas extends JPanel
+ implements MouseListener, MouseMotionListener, StructureListener
{
boolean redrawneeded = true;
for (int i = 0; i < pdb.getChains().size(); i++)
{
- mappingDetails
- .append("\n\nPDB Sequence is :\nSequence = "
- + pdb.getChains().elementAt(i).sequence
- .getSequenceAsString());
+ mappingDetails.append("\n\nPDB Sequence is :\nSequence = "
+ + pdb.getChains().elementAt(i).sequence
+ .getSequenceAsString());
mappingDetails.append("\nNo of residues = "
+ pdb.getChains().elementAt(i).residues.size() + "\n\n");
if (pos > 0)
{
pos = sequence[s].findIndex(pos);
- tmp.endCol = sr
- .getResidueColour(sequence[s], pos, finder);
+ tmp.endCol = sr.getResidueColour(sequence[s], pos,
+ finder);
}
}
{
tmpBond = visiblebonds.elementAt(i);
- xstart = (int) (((tmpBond.start[0] - centre[0]) * scale) + (getWidth() / 2));
- ystart = (int) (((centre[1] - tmpBond.start[1]) * scale) + (getHeight() / 2));
+ xstart = (int) (((tmpBond.start[0] - centre[0]) * scale)
+ + (getWidth() / 2));
+ ystart = (int) (((centre[1] - tmpBond.start[1]) * scale)
+ + (getHeight() / 2));
- xend = (int) (((tmpBond.end[0] - centre[0]) * scale) + (getWidth() / 2));
- yend = (int) (((centre[1] - tmpBond.end[1]) * scale) + (getHeight() / 2));
+ xend = (int) (((tmpBond.end[0] - centre[0]) * scale)
+ + (getWidth() / 2));
+ yend = (int) (((centre[1] - tmpBond.end[1]) * scale)
+ + (getHeight() / 2));
xmid = (xend + xstart) / 2;
ymid = (yend + ystart) / 2;
if (highlightBond1 != null && highlightBond1 == tmpBond)
{
- g.setColor(tmpBond.endCol.brighter().brighter().brighter()
- .brighter());
+ g.setColor(
+ tmpBond.endCol.brighter().brighter().brighter().brighter());
drawLine(g, xmid, ymid, xend, yend);
}
if (fatom != null)
{
- this.setToolTipText(chain.id + ":" + fatom.resNumber + " "
- + fatom.resName);
+ this.setToolTipText(
+ chain.id + ":" + fatom.resNumber + " " + fatom.resName);
}
else
{
g.setColor(Color.red);
if (n == 1)
{
- int xstart = (int) (((b.start[0] - centre[0]) * scale) + (getWidth() / 2));
- int ystart = (int) (((centre[1] - b.start[1]) * scale) + (getHeight() / 2));
+ int xstart = (int) (((b.start[0] - centre[0]) * scale)
+ + (getWidth() / 2));
+ int ystart = (int) (((centre[1] - b.start[1]) * scale)
+ + (getHeight() / 2));
g.drawString(b.at1.resName + "-" + b.at1.resNumber, xstart, ystart);
}
if (n == 2)
{
- int xstart = (int) (((b.end[0] - centre[0]) * scale) + (getWidth() / 2));
- int ystart = (int) (((centre[1] - b.end[1]) * scale) + (getHeight() / 2));
+ int xstart = (int) (((b.end[0] - centre[0]) * scale)
+ + (getWidth() / 2));
+ int ystart = (int) (((centre[1] - b.end[1]) * scale)
+ + (getHeight() / 2));
g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart);
}
{
tmpBond = bond;
- truex = (int) (((tmpBond.start[0] - centre[0]) * scale) + (getWidth() / 2));
+ truex = (int) (((tmpBond.start[0] - centre[0]) * scale)
+ + (getWidth() / 2));
if (Math.abs(truex - x) <= 2)
{
- int truey = (int) (((centre[1] - tmpBond.start[1]) * scale) + (getHeight() / 2));
+ int truey = (int) (((centre[1] - tmpBond.start[1]) * scale)
+ + (getHeight() / 2));
if (Math.abs(truey - y) <= 2)
{
// Still here? Maybe its the last bond
- truex = (int) (((tmpBond.end[0] - centre[0]) * scale) + (getWidth() / 2));
+ truex = (int) (((tmpBond.end[0] - centre[0]) * scale)
+ + (getWidth() / 2));
if (Math.abs(truex - x) <= 2)
{
- int truey = (int) (((tmpBond.end[1] - centre[1]) * scale) + (getHeight() / 2));
+ int truey = (int) (((tmpBond.end[1] - centre[1]) * scale)
+ + (getHeight() / 2));
if (Math.abs(truey - y) <= 2)
{
tx.setEnd(1 + residues.elementAt(tx.getEnd() - offset).atoms
.elementAt(0).alignmentMapping);
tx.setStatus(status
- + ((tx.getStatus() == null || tx.getStatus().length() == 0) ? ""
+ + ((tx.getStatus() == null || tx.getStatus().length() == 0)
+ ? ""
: ":" + tx.getStatus()));
if (tx.begin != 0 && tx.end != 0)
{
// Add inserted residues as features to the base residue
Atom currAtom = resAtoms.get(0);
- if (currAtom.insCode != ' '
- && !residues.isEmpty()
- && residues.lastElement().atoms.get(0).resNumber == currAtom.resNumber)
+ if (currAtom.insCode != ' ' && !residues.isEmpty()
+ && residues.lastElement().atoms
+ .get(0).resNumber == currAtom.resNumber)
{
SequenceFeature sf = new SequenceFeature("INSERTION",
currAtom.resName + ":" + currAtom.resNumIns + " " + pdbid
- + id, "", offset + count - 1, offset + count - 1,
- "PDB_INS");
+ + id,
+ "", offset + count - 1, offset + count - 1, "PDB_INS");
resFeatures.addElement(sf);
residues.lastElement().atoms.addAll(resAtoms);
}
Residue tmpres = residues.lastElement();
Atom tmpat = tmpres.atoms.get(0);
// Make A new SequenceFeature for the current residue numbering
- SequenceFeature sf = new SequenceFeature(RESNUM_FEATURE, tmpat.resName
- + ":" + tmpat.resNumIns + " " + pdbid + id, "", offset
- + count, offset + count, pdbid);
+ SequenceFeature sf = new SequenceFeature(RESNUM_FEATURE,
+ tmpat.resName + ":" + tmpat.resNumIns + " " + pdbid + id,
+ "", offset + count, offset + count, pdbid);
resFeatures.addElement(sf);
resAnnotation.addElement(new Annotation(tmpat.tfactor));
// Keep totting up the sequence
- if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null)
+ if ((symbol = ResidueProperties.getAA3Hash()
+ .get(tmpat.resName)) == null)
{
String nucname = tmpat.resName.trim();
// use the aaIndex rather than call 'toLower' - which would take a bit
// more time.
deoxyn = nucname.length() == 2
- && ResidueProperties.aaIndex[nucname.charAt(0)] == ResidueProperties.aaIndex['D'];
+ && ResidueProperties.aaIndex[nucname
+ .charAt(0)] == ResidueProperties.aaIndex['D'];
if (tmpat.name.equalsIgnoreCase("CA")
|| ResidueProperties.nucleotideIndex[nucname
.charAt((deoxyn ? 1 : 0))] == -1)
{
- char r = ResidueProperties
- .getSingleCharacterCode(ResidueProperties
- .getCanonicalAminoAcid(tmpat.resName));
+ char r = ResidueProperties.getSingleCharacterCode(
+ ResidueProperties.getCanonicalAminoAcid(tmpat.resName));
seq.append(r == '0' ? 'X' : r);
// System.err.println("PDBReader:Null aa3Hash for " +
// tmpat.resName);
{
if (nucleotide)
{
- System.err
- .println("Warning: mixed nucleotide and amino acid chain.. its gonna do bad things to you!");
+ System.err.println(
+ "Warning: mixed nucleotide and amino acid chain.. its gonna do bad things to you!");
}
seq.append(ResidueProperties.aa[((Integer) symbol).intValue()]);
}
try
{
index = ResidueProperties.aa3Hash.get(b.at1.resName).intValue();
- b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0),
- 0, null, null, 0f);
+ b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0), 0,
+ null, null, 0f);
index = ResidueProperties.aa3Hash.get(b.at2.resName).intValue();
b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0), 0,
for (AlignmentAnnotation ana : shadow.getAnnotation())
{
- List<AlignmentAnnotation> transfer = sq.getAlignmentAnnotations(
- ana.getCalcId(), ana.label);
+ List<AlignmentAnnotation> transfer = sq
+ .getAlignmentAnnotations(ana.getCalcId(), ana.label);
if (transfer == null || transfer.size() == 0)
{
ana = new AlignmentAnnotation(ana);
// Useful for debugging mappings - adds annotation for mapped position
float min = -1, max = 0;
Annotation[] an = new Annotation[sq.getEnd() - sq.getStart() + 1];
- for (int i = sq.getStart(), j = sq.getEnd(), k = 0; i <= j; i++, k++)
+ for (int i = sq.getStart(), j = sq
+ .getEnd(), k = 0; i <= j; i++, k++)
{
int prn = mapping.getPDBResNum(k + 1);
public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
boolean externalSecStr, String dataObject,
- DataSourceType sourceType)
- throws IOException
+ DataSourceType sourceType) throws IOException
{
super(false, dataObject, sourceType);
addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
} catch (OutOfMemoryError er)
{
System.out.println("OUT OF MEMORY LOADING PDB FILE");
- throw new IOException(
- MessageManager
- .getString("exception.outofmemory_loading_pdb_file"));
+ throw new IOException(MessageManager
+ .getString("exception.outofmemory_loading_pdb_file"));
} catch (NumberFormatException ex)
{
if (line != null)
public static String relocateCalcId(String calcId,
Hashtable<String, String> alreadyLoadedPDB) throws Exception
{
- int s = CALC_ID_PREFIX.length(), end = calcId
- .indexOf(CALC_ID_PREFIX, s);
+ int s = CALC_ID_PREFIX.length(),
+ end = calcId.indexOf(CALC_ID_PREFIX, s);
String between = calcId.substring(s, end - 1);
return CALC_ID_PREFIX + alreadyLoadedPDB.get(between) + ":"
+ calcId.substring(end);
{
if (sequences[row] == null)
{
- System.err
- .println("WARNING: Consensus skipping null sequence - possible race condition.");
+ System.err.println(
+ "WARNING: Consensus skipping null sequence - possible race condition.");
continue;
}
char[] seq = sequences[row].getSequence();
// always set ranges again
gaprow.graphMax = nseq;
gaprow.graphMin = 0;
- double scale = 0.8/nseq;
+ double scale = 0.8 / nseq;
for (int i = startCol; i < endCol; i++)
{
ProfileI profile = profiles.get(i);
String description = "" + gapped;
- gaprow.annotations[i] = new Annotation("", description,
- '\0', gapped, jalview.util.ColorUtils.bleachColour(
- Color.DARK_GRAY, (float) scale * gapped));
+ gaprow.annotations[i] = new Annotation("", description, '\0', gapped,
+ jalview.util.ColorUtils.bleachColour(Color.DARK_GRAY,
+ (float) scale * gapped));
}
}
* <ul>
* <li>the full profile (percentages of all residues present), if
* showSequenceLogo is true, or</li>
- * <li>just the modal (most common) residue(s), if showSequenceLogo is false</li>
+ * <li>just the modal (most common) residue(s), if showSequenceLogo is
+ * false</li>
* </ul>
* Percentages are as a fraction of all sequence, or only ungapped sequences
* if ignoreGaps is true.
String description = null;
if (counts != null && showSequenceLogo)
{
- int normaliseBy = ignoreGaps ? profile.getNonGapped() : profile
- .getHeight();
+ int normaliseBy = ignoreGaps ? profile.getNonGapped()
+ : profile.getHeight();
description = counts.getTooltip(normaliseBy, dp);
}
else
QuickSort.sort(values, symbols);
int nextArrayPos = 2;
int totalPercentage = 0;
- final int divisor = ignoreGaps ? profile.getNonGapped() : profile
- .getHeight();
+ final int divisor = ignoreGaps ? profile.getNonGapped()
+ : profile.getHeight();
/*
* traverse the arrays in reverse order (highest counts first)
{
continue;
}
- List<char[]> codons = MappingUtils
- .findCodonsFor(seq, col, mappings);
+ List<char[]> codons = MappingUtils.findCodonsFor(seq, col,
+ mappings);
for (char[] codon : codons)
{
int codonEncoded = CodingUtils.encodeCodon(codon);
int modalCodonEncoded = codons[codons.length - 1];
int modalCodonCount = sortedCodonCounts[codons.length - 1];
- String modalCodon = String.valueOf(CodingUtils
- .decodeCodon(modalCodonEncoded));
- if (sortedCodonCounts.length > 1
- && sortedCodonCounts[codons.length - 2] == sortedCodonCounts[codons.length - 1])
+ String modalCodon = String
+ .valueOf(CodingUtils.decodeCodon(modalCodonEncoded));
+ if (sortedCodonCounts.length > 1 && sortedCodonCounts[codons.length
+ - 2] == sortedCodonCounts[codons.length - 1])
{
/*
* two or more codons share the modal count
{
if (samePercent.length() > 0)
{
- mouseOver.append(samePercent).append(": ")
- .append(lastPercent).append("% ");
+ mouseOver.append(samePercent).append(": ").append(lastPercent)
+ .append("% ");
}
samePercent.setLength(0);
samePercent.append(codon);
/**
* Creates a new AlignSeq object.
*
- * @param s1 first sequence for alignment
- * @param s2 second sequence for alignment
- * @param type molecule type, either AlignSeq.PEP or AlignSeq.DNA
+ * @param s1
+ * first sequence for alignment
+ * @param s2
+ * second sequence for alignment
+ * @param type
+ * molecule type, either AlignSeq.PEP or AlignSeq.DNA
*/
public AlignSeq(SequenceI s1, SequenceI s2, String type)
{
SequenceI alSeq1 = new Sequence(s1.getName(), getAStr1());
alSeq1.setStart(s1.getStart() + getSeq1Start() - 1);
alSeq1.setEnd(s1.getStart() + getSeq1End() - 1);
- alSeq1.setDatasetSequence(s1.getDatasetSequence() == null ? s1 : s1
- .getDatasetSequence());
+ alSeq1.setDatasetSequence(
+ s1.getDatasetSequence() == null ? s1 : s1.getDatasetSequence());
return alSeq1;
}
SequenceI alSeq2 = new Sequence(s2.getName(), getAStr2());
alSeq2.setStart(s2.getStart() + getSeq2Start() - 1);
alSeq2.setEnd(s2.getStart() + getSeq2End() - 1);
- alSeq2.setDatasetSequence(s2.getDatasetSequence() == null ? s2 : s2
- .getDatasetSequence());
+ alSeq2.setDatasetSequence(
+ s2.getDatasetSequence() == null ? s2 : s2.getDatasetSequence());
return alSeq2;
}
if (s1str.length() == 0 || s2str.length() == 0)
{
- output.append("ALL GAPS: "
- + (s1str.length() == 0 ? s1.getName() : " ")
- + (s2str.length() == 0 ? s2.getName() : ""));
+ output.append(
+ "ALL GAPS: " + (s1str.length() == 0 ? s1.getName() : " ")
+ + (s2str.length() == 0 ? s2.getName() : ""));
return;
}
if (!PEP.equals(moleculeType) && !DNA.equals(moleculeType))
{
output.append("Wrong type = dna or pep only");
- throw new Error(MessageManager.formatMessage(
- "error.unknown_type_dna_or_pep",
- new String[] { moleculeType }));
+ throw new Error(MessageManager
+ .formatMessage("error.unknown_type_dna_or_pep", new String[]
+ { moleculeType }));
}
type = moleculeType;
- scoreMatrix = ScoreModels.getInstance().getDefaultModel(
- PEP.equals(type));
+ scoreMatrix = ScoreModels.getInstance()
+ .getDefaultModel(PEP.equals(type));
}
/**
float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(i),
s2str.charAt(j));
- score[i][j] = max(score[i - 1][j - 1]
- + (pairwiseScore * 10), E[i][j], F[i][j]);
+ score[i][j] = max(score[i - 1][j - 1] + (pairwiseScore * 10),
+ E[i][j], F[i][j]);
traceback[i][j] = findTrace(i, j);
}
}
*/
public jalview.datamodel.Mapping getMappingFromS1(boolean allowmismatch)
{
- ArrayList<Integer> as1 = new ArrayList<Integer>(), as2 = new ArrayList<Integer>();
+ ArrayList<Integer> as1 = new ArrayList<Integer>(),
+ as2 = new ArrayList<Integer>();
int pdbpos = s2.getStart() + getSeq2Start() - 2;
int alignpos = s1.getStart() + getSeq1Start() - 2;
int lp2 = pdbpos - 3, lp1 = alignpos - 3;
}
// construct range pairs
- int[] mapseq1 = new int[as1.size() + (lastmatch ? 1 : 0)], mapseq2 = new int[as2
- .size() + (lastmatch ? 1 : 0)];
+ int[] mapseq1 = new int[as1.size() + (lastmatch ? 1 : 0)],
+ mapseq2 = new int[as2.size() + (lastmatch ? 1 : 0)];
int i = 0;
for (Integer ip : as1)
{
List<SequenceI> ochains, AlignmentI al, String dnaOrProtein,
boolean removeOldAnnots)
{
- List<SequenceI> orig = new ArrayList<SequenceI>(), repl = new ArrayList<SequenceI>();
+ List<SequenceI> orig = new ArrayList<SequenceI>(),
+ repl = new ArrayList<SequenceI>();
List<AlignSeq> aligs = new ArrayList<AlignSeq>();
if (al != null && al.getHeight() > 0)
{
{
continue;
}
- if (forSequences != null
- && (aa.sequenceRef != null && forSequences
- .contains(aa.sequenceRef)))
+ if (forSequences != null && (aa.sequenceRef != null
+ && forSequences.contains(aa.sequenceRef)))
{
String calcId = aa.getCalcId();
.get(calcId);
if (groupLabelsForCalcId.containsKey(aa.graphGroup))
{
- if (!groupLabelsForCalcId.get(aa.graphGroup).contains(
- displayLabel))
+ if (!groupLabelsForCalcId.get(aa.graphGroup)
+ .contains(displayLabel))
{
groupLabelsForCalcId.get(aa.graphGroup).add(displayLabel);
}
true);
for (int i = 0; i < nSeq; i++)
{
- scores[i] = (float) PIDModel.computePID(align.getSequenceAt(i)
- .getSequenceAsString(), refSeq, pidParams);
+ scores[i] = (float) PIDModel.computePID(
+ align.getSequenceAt(i).getSequenceAsString(), refSeq,
+ pidParams);
seqs[i] = align.getSequenceAt(i);
}
}
else
{
- setReverseOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
+ setReverseOrder(align,
+ vectorSubsetToArray(tmp, align.getSequences()));
}
}
if (tmp.size() != nSeq)
{
- System.err
- .println("WARNING: tmp.size()="
- + tmp.size()
- + " != nseq="
- + nSeq
- + " in getOrderByTree - tree contains sequences not in alignment");
+ System.err.println("WARNING: tmp.size()=" + tmp.size() + " != nseq="
+ + nSeq
+ + " in getOrderByTree - tree contains sequences not in alignment");
}
}
}
else
{
- setReverseOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
+ setReverseOrder(align,
+ vectorSubsetToArray(tmp, align.getSequences()));
}
}
int start, int stop, AlignmentI alignment, String method)
{
sortByFeature(
- featureLabel == null ? null
- : Arrays.asList(new String[] { featureLabel }),
- groupLabel == null ? null : Arrays
- .asList(new String[] { groupLabel }), start, stop,
- alignment, method);
+ featureLabel == null ? null : Arrays.asList(new String[]
+ { featureLabel }),
+ groupLabel == null ? null : Arrays.asList(new String[]
+ { groupLabel }), start, stop, alignment, method);
}
private static boolean containsIgnoreCase(final String lab,
if (method != FEATURE_SCORE && method != FEATURE_LABEL
&& method != FEATURE_DENSITY)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_sortbyfeature"));
+ throw new Error(MessageManager
+ .getString("error.implementation_error_sortbyfeature"));
}
boolean ignoreScore = method != FEATURE_SCORE;
*/
boolean noOverlap = seqs[i].findIndex(feature.getBegin()) > stop + 1
|| seqs[i].findIndex(feature.getEnd()) < start + 1;
- boolean skipFeatureType = featureLabels != null
- && !AlignmentSorter.containsIgnoreCase(feature.type,
- featureLabels);
+ boolean skipFeatureType = featureLabels != null && !AlignmentSorter
+ .containsIgnoreCase(feature.type, featureLabels);
boolean skipFeatureGroup = groupLabels != null
- && (feature.getFeatureGroup() != null && !AlignmentSorter
- .containsIgnoreCase(feature.getFeatureGroup(),
- groupLabels));
+ && (feature.getFeatureGroup() != null
+ && !AlignmentSorter.containsIgnoreCase(
+ feature.getFeatureGroup(), groupLabels));
if (noOverlap || skipFeatureType || skipFeatureGroup)
{
// forget about this feature
String[] labs = new String[fs.length];
for (int l = 0; l < labs.length; l++)
{
- labs[l] = (fs[l].getDescription() != null ? fs[l]
- .getDescription() : fs[l].getType());
+ labs[l] = (fs[l].getDescription() != null
+ ? fs[l].getDescription()
+ : fs[l].getType());
}
QuickSort.sort(labs, ((Object[]) feats[i]));
}
}
}
// TODO use Character.toLowerCase to avoid creating String objects?
- char[] upstream = new String(ds.getSequence(s.getStart() - 1
- - ustream_ds, s.getStart() - 1)).toLowerCase().toCharArray();
- char[] downstream = new String(ds.getSequence(s_end - 1, s_end
- + dstream_ds)).toLowerCase().toCharArray();
+ char[] upstream = new String(ds
+ .getSequence(s.getStart() - 1 - ustream_ds, s.getStart() - 1))
+ .toLowerCase().toCharArray();
+ char[] downstream = new String(
+ ds.getSequence(s_end - 1, s_end + dstream_ds)).toLowerCase()
+ .toCharArray();
char[] coreseq = s.getSequence();
char[] nseq = new char[offset + upstream.length + downstream.length
+ coreseq.length];
System.arraycopy(upstream, 0, nseq, p, upstream.length);
System.arraycopy(coreseq, 0, nseq, p + upstream.length,
coreseq.length);
- System.arraycopy(downstream, 0, nseq, p + coreseq.length
- + upstream.length, downstream.length);
+ System.arraycopy(downstream, 0, nseq,
+ p + coreseq.length + upstream.length, downstream.length);
s.setSequence(new String(nseq));
s.setStart(s.getStart() - ustream_ds);
s.setEnd(s_end + downstream.length);
* @return
*/
protected static boolean mapProteinToCdna(
- final AlignmentI proteinAlignment,
- final AlignmentI cdnaAlignment, Set<SequenceI> mappedDna,
- Set<SequenceI> mappedProtein, boolean xrefsOnly)
+ final AlignmentI proteinAlignment, final AlignmentI cdnaAlignment,
+ Set<SequenceI> mappedDna, Set<SequenceI> mappedProtein,
+ boolean xrefsOnly)
{
boolean mappingExistsOrAdded = false;
List<SequenceI> thisSeqs = proteinAlignment.getSequences();
* Don't map non-xrefd sequences more than once each. This heuristic
* allows us to pair up similar sequences in ordered alignments.
*/
- if (!xrefsOnly
- && (mappedProtein.contains(aaSeq) || mappedDna
- .contains(cdnaSeq)))
+ if (!xrefsOnly && (mappedProtein.contains(aaSeq)
+ || mappedDna.contains(cdnaSeq)))
{
continue;
}
/**
* Builds a mapping (if possible) of a cDNA to a protein sequence.
* <ul>
- * <li>first checks if the cdna translates exactly to the protein sequence</li>
+ * <li>first checks if the cdna translates exactly to the protein
+ * sequence</li>
* <li>else checks for translation after removing a STOP codon</li>
* <li>else checks for translation after removing a START codon</li>
* <li>if that fails, inspect CDS features on the cDNA sequence</li>
* String objects.
*/
final SequenceI proteinDataset = proteinSeq.getDatasetSequence();
- char[] aaSeqChars = proteinDataset != null ? proteinDataset
- .getSequence() : proteinSeq.getSequence();
+ char[] aaSeqChars = proteinDataset != null
+ ? proteinDataset.getSequence()
+ : proteinSeq.getSequence();
final SequenceI cdnaDataset = cdnaSeq.getDatasetSequence();
char[] cdnaSeqChars = cdnaDataset != null ? cdnaDataset.getSequence()
: cdnaSeq.getSequence();
* If lengths still don't match, try ignoring start codon.
*/
int startOffset = 0;
- if (cdnaLength != mappedLength
- && cdnaLength > 2
+ if (cdnaLength != mappedLength && cdnaLength > 2
&& String.valueOf(cdnaSeqChars, 0, CODON_LENGTH).toUpperCase()
.equals(ResidueProperties.START))
{
/*
* protein is translation of dna (+/- start/stop codons)
*/
- MapList map = new MapList(new int[] { cdnaStart, cdnaEnd }, new int[]
- { proteinStart, proteinEnd }, CODON_LENGTH, 1);
+ MapList map = new MapList(new int[] { cdnaStart, cdnaEnd },
+ new int[]
+ { proteinStart, proteinEnd }, CODON_LENGTH, 1);
return map;
}
int aaPos = 0;
int dnaPos = cdnaStart;
- for (; dnaPos < cdnaSeqChars.length - 2 && aaPos < aaSeqChars.length; dnaPos += CODON_LENGTH, aaPos++)
+ for (; dnaPos < cdnaSeqChars.length - 2
+ && aaPos < aaSeqChars.length; dnaPos += CODON_LENGTH, aaPos++)
{
String codon = String.valueOf(cdnaSeqChars, dnaPos, CODON_LENGTH);
final String translated = ResidueProperties.codonTranslate(codon);
* @param preserveUnmappedGaps
* @param preserveMappedGaps
*/
- public static void alignSequenceAs(SequenceI alignTo,
- SequenceI alignFrom, AlignedCodonFrame mapping, String myGap,
- char sourceGap, boolean preserveMappedGaps,
- boolean preserveUnmappedGaps)
+ public static void alignSequenceAs(SequenceI alignTo, SequenceI alignFrom,
+ AlignedCodonFrame mapping, String myGap, char sourceGap,
+ boolean preserveMappedGaps, boolean preserveUnmappedGaps)
{
// TODO generalise to work for Protein-Protein, dna-dna, dna-protein
}
else
{
- gapsToAdd = Math.min(intronLength + trailingGapLength
- - sourceGapMappedLength, trailingGapLength);
+ gapsToAdd = Math.min(
+ intronLength + trailingGapLength - sourceGapMappedLength,
+ trailingGapLength);
}
}
}
* @return
*/
static boolean alignCdsSequenceAsProtein(SequenceI cdsSeq,
- AlignmentI protein, List<AlignedCodonFrame> mappings, char gapChar)
+ AlignmentI protein, List<AlignedCodonFrame> mappings,
+ char gapChar)
{
SequenceI cdsDss = cdsSeq.getDatasetSequence();
if (cdsDss == null)
mapList = mapList.getInverse();
}
int cdsLength = cdsDss.getLength();
- int mappedFromLength = MappingUtils.getLength(mapList
- .getFromRanges());
+ int mappedFromLength = MappingUtils
+ .getLength(mapList.getFromRanges());
int mappedToLength = MappingUtils
.getLength(mapList.getToRanges());
boolean addStopCodon = (cdsLength == mappedFromLength
* CODON_LENGTH + CODON_LENGTH)
- || (peptide.getDatasetSequence().getLength() == mappedFromLength - 1);
+ || (peptide.getDatasetSequence()
+ .getLength() == mappedFromLength - 1);
if (cdsLength != mappedToLength && !addStopCodon)
{
- System.err
- .println(String
- .format("Can't align cds as protein (length mismatch %d/%d): %s",
- cdsLength, mappedToLength,
- cdsSeq.getName()));
+ System.err.println(String.format(
+ "Can't align cds as protein (length mismatch %d/%d): %s",
+ cdsLength, mappedToLength, cdsSeq.getName()));
}
/*
break;
}
}
- for (int i = nucleotides.length - CODON_LENGTH; i < nucleotides.length; i++)
+ for (int i = nucleotides.length
+ - CODON_LENGTH; i < nucleotides.length; i++)
{
alignedCds[cdsCol++] = nucleotides[i];
}
if (prot != null)
{
Mapping seqMap = mapping.getMappingForSequence(dnaSeq);
- addCodonPositions(dnaSeq, prot, protein.getGapCharacter(),
- seqMap, alignedCodons);
+ addCodonPositions(dnaSeq, prot, protein.getGapCharacter(), seqMap,
+ alignedCodons);
unmappedProtein.remove(prot);
}
}
AlignedCodon codon = sequenceCodon.getValue();
if (codon.peptideCol > 1)
{
- System.err
- .println("Problem mapping protein with >1 unmapped start positions: "
+ System.err.println(
+ "Problem mapping protein with >1 unmapped start positions: "
+ seq.getName());
}
else if (codon.peptideCol == 1)
if (lastCodon != null)
{
AlignedCodon firstPeptide = new AlignedCodon(lastCodon.pos1,
- lastCodon.pos2, lastCodon.pos3, String.valueOf(seq
- .getCharAt(0)), 0);
+ lastCodon.pos2, lastCodon.pos3,
+ String.valueOf(seq.getCharAt(0)), 0);
toAdd.put(seq, firstPeptide);
}
else
* <ul>
* <li>One alignment must be nucleotide, and the other protein</li>
* <li>At least one pair of sequences must be already mapped, or mappable</li>
- * <li>Mappable means the nucleotide translation matches the protein sequence</li>
+ * <li>Mappable means the nucleotide translation matches the protein
+ * sequence</li>
* <li>The translation may ignore start and stop codons if present in the
* nucleotide</li>
* </ul>
return false;
}
- SequenceI dnaDs = dnaSeq.getDatasetSequence() == null ? dnaSeq : dnaSeq
- .getDatasetSequence();
- SequenceI proteinDs = proteinSeq.getDatasetSequence() == null ? proteinSeq
+ SequenceI dnaDs = dnaSeq.getDatasetSequence() == null ? dnaSeq
+ : dnaSeq.getDatasetSequence();
+ SequenceI proteinDs = proteinSeq.getDatasetSequence() == null
+ ? proteinSeq
: proteinSeq.getDatasetSequence();
for (AlignedCodonFrame mapping : mappings)
* the alignment to check for presence of annotations
*/
public static void findAddableReferenceAnnotations(
- List<SequenceI> sequenceScope,
- Map<String, String> labelForCalcId,
+ List<SequenceI> sequenceScope, Map<String, String> labelForCalcId,
final Map<SequenceI, List<AlignmentAnnotation>> candidates,
AlignmentI al)
{
/**
* Set visibility of alignment annotations of specified types (labels), for
- * specified sequences. This supports controls like
- * "Show all secondary structure", "Hide all Temp factor", etc.
+ * specified sequences. This supports controls like "Show all secondary
+ * structure", "Hide all Temp factor", etc.
*
* @al the alignment to scan for annotations
* @param types
{
if (anyType || types.contains(aa.label))
{
- if ((aa.sequenceRef != null)
- && (forSequences == null || forSequences
- .contains(aa.sequenceRef)))
+ if ((aa.sequenceRef != null) && (forSequences == null
+ || forSequences.contains(aa.sequenceRef)))
{
aa.visible = doShow;
}
productSeqs = new HashSet<SequenceI>();
for (SequenceI seq : products)
{
- productSeqs.add(seq.getDatasetSequence() == null ? seq : seq
- .getDatasetSequence());
+ productSeqs.add(seq.getDatasetSequence() == null ? seq
+ : seq.getDatasetSequence());
}
}
/*
* add a mapping from CDS to the (unchanged) mapped to range
*/
- List<int[]> cdsRange = Collections.singletonList(new int[] { 1,
- cdsSeq.getLength() });
+ List<int[]> cdsRange = Collections
+ .singletonList(new int[]
+ { 1, cdsSeq.getLength() });
MapList cdsToProteinMap = new MapList(cdsRange,
mapList.getToRanges(), mapList.getFromRatio(),
mapList.getToRatio());
// 'CDS|emblcdsacc'
// assuming cds version same as dna ?!?
- DBRefEntry proteinToCdsRef = new DBRefEntry(
- primRef.getSource(), primRef.getVersion(),
- cdsSeq.getName());
+ DBRefEntry proteinToCdsRef = new DBRefEntry(primRef.getSource(),
+ primRef.getVersion(), cdsSeq.getName());
//
- proteinToCdsRef.setMap(new Mapping(cdsSeqDss, cdsToProteinMap
- .getInverse()));
+ proteinToCdsRef.setMap(
+ new Mapping(cdsSeqDss, cdsToProteinMap.getInverse()));
proteinProduct.addDBRef(proteinToCdsRef);
}
}
}
- AlignmentI cds = new Alignment(cdsSeqs.toArray(new SequenceI[cdsSeqs
- .size()]));
+ AlignmentI cds = new Alignment(
+ cdsSeqs.toArray(new SequenceI[cdsSeqs.size()]));
cds.setDataset(dataset);
return cds;
* is this mapping from the whole dna sequence (i.e. CDS)?
* allowing for possible stop codon on dna but not peptide
*/
- int mappedFromLength = MappingUtils.getLength(aMapping.getMap()
- .getFromRanges());
+ int mappedFromLength = MappingUtils
+ .getLength(aMapping.getMap().getFromRanges());
int dnaLength = seqDss.getLength();
if (mappedFromLength == dnaLength
|| mappedFromLength == dnaLength - CODON_LENGTH)
&& proteinProduct == mapping.getTo()
&& seqDss != map.getFromSeq())
{
- mappedFromLength = MappingUtils.getLength(mapping.getMap()
- .getFromRanges());
+ mappedFromLength = MappingUtils
+ .getLength(mapping.getMap().getFromRanges());
if (mappedFromLength == map.getFromSeq().getLength())
{
/*
}
else
{
- System.err
- .println("JAL-2154 regression: warning - found (and ignnored a duplicate CDS sequence):"
+ System.err.println(
+ "JAL-2154 regression: warning - found (and ignnored a duplicate CDS sequence):"
+ mtch.toString());
}
}
for (DBRefEntry cdsref : direct)
{
// clone maplist and mapping
- MapList cdsposmap = new MapList(Arrays.asList(new int[][] { new int[]
- { cdsSeq.getStart(), cdsSeq.getEnd() } }), cdsref.getMap().getMap()
- .getToRanges(), 3, 1);
- Mapping cdsmap = new Mapping(cdsref.getMap().getTo(), cdsref.getMap()
- .getMap());
+ MapList cdsposmap = new MapList(
+ Arrays.asList(new int[][]
+ { new int[] { cdsSeq.getStart(), cdsSeq.getEnd() } }),
+ cdsref.getMap().getMap().getToRanges(), 3, 1);
+ Mapping cdsmap = new Mapping(cdsref.getMap().getTo(),
+ cdsref.getMap().getMap());
// create dbref
DBRefEntry newref = new DBRefEntry(cdsref.getSource(),
- cdsref.getVersion(), cdsref.getAccessionId(), new Mapping(
- cdsmap.getTo(), cdsposmap));
+ cdsref.getVersion(), cdsref.getAccessionId(),
+ new Mapping(cdsmap.getTo(), cdsposmap));
// and see if we can map to the protein product for this mapping.
// onSource is the filtered set of accessions on protein that we are
if (begin > end)
{
// shouldn't happen!
- System.err
- .println("Error: start phase extends beyond start CDS in "
+ System.err.println(
+ "Error: start phase extends beyond start CDS in "
+ dnaSeq.getName());
}
}
* are currently ignored here
*/
String trans = codon.contains("-") ? "-"
- : (codon.length() > CODON_LENGTH ? null : ResidueProperties
- .codonTranslate(codon));
+ : (codon.length() > CODON_LENGTH ? null
+ : ResidueProperties.codonTranslate(codon));
if (trans != null && !trans.equals(residue))
{
String residue3Char = StringUtils
StringBuilder link = new StringBuilder(32);
try
{
- link.append(desc)
- .append(" ")
- .append(id)
- .append("|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=")
+ link.append(desc).append(" ").append(id).append(
+ "|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=")
.append(URLEncoder.encode(id, "UTF-8"));
sf.addLink(link.toString());
} catch (UnsupportedEncodingException e)
* get this peptide's codon positions e.g. [3, 4, 5] or [4, 7, 10]
*/
int[] codon = peptidePosition == lastPeptidePostion ? lastCodon
- : MappingUtils.flattenRanges(dnaToProtein.locateInFrom(
- peptidePosition, peptidePosition));
+ : MappingUtils.flattenRanges(dnaToProtein
+ .locateInFrom(peptidePosition, peptidePosition));
lastPeptidePostion = peptidePosition;
lastCodon = codon;
*/
for (int codonPos = 0; codonPos < CODON_LENGTH; codonPos++)
{
- String nucleotide = String.valueOf(
- dnaSeq.getCharAt(codon[codonPos] - dnaStart))
+ String nucleotide = String
+ .valueOf(dnaSeq.getCharAt(codon[codonPos] - dnaStart))
.toUpperCase();
List<DnaVariant> codonVariant = codonVariants[codonPos];
if (codon[codonPos] == dnaCol)
*/
for (SequenceI seq : unaligned.getSequences())
{
- List<SequenceI> alignedSequences = alignedDatasets.get(seq
- .getDatasetSequence());
+ List<SequenceI> alignedSequences = alignedDatasets
+ .get(seq.getDatasetSequence());
// TODO: getSequenceAsString() will be deprecated in the future
// TODO: need to leave to SequenceI implementor to update gaps
seq.setSequence(alignedSequences.get(0).getSequenceAsString());
* @return
*/
static SortedMap<Integer, Map<SequenceI, Character>> buildMappedColumnsMap(
- AlignmentI unaligned, AlignmentI aligned, List<SequenceI> unmapped)
+ AlignmentI unaligned, AlignmentI aligned,
+ List<SequenceI> unmapped)
{
/*
* Map will hold, for each aligned column position, a map of
}
/**
- * Helper method that adds to a map the mapped column positions of a sequence. <br>
+ * Helper method that adds to a map the mapped column positions of a sequence.
+ * <br>
* For example if aaTT-Tg-gAAA is mapped to TTTAAA then the map should record
* that columns 3,4,6,10,11,12 map to characters T,T,T,A,A,A of the mapped to
* sequence.
*/
if (seqMap.getTo() == fromSeq.getDatasetSequence())
{
- seqMap = new Mapping(seq.getDatasetSequence(), seqMap.getMap()
- .getInverse());
+ seqMap = new Mapping(seq.getDatasetSequence(),
+ seqMap.getMap().getInverse());
}
char[] fromChars = fromSeq.getSequence();
public enum SequenceAnnotationOrder
{
// Text descriptions surface in the Preferences Sort by... options
- SEQUENCE_AND_LABEL("Sequence"), LABEL_AND_SEQUENCE("Label"), NONE(
- "No sort");
+ SEQUENCE_AND_LABEL("Sequence"), LABEL_AND_SEQUENCE("Label"),
+ NONE("No sort");
private String description;
* <ul>
* <li>annotations with a reference to a sequence in the alignment are sorted
* on sequence ordering</li>
- * <li>other annotations go 'at the end', with their mutual order unchanged</li>
+ * <li>other annotations go 'at the end', with their mutual order
+ * unchanged</li>
* <li>within the same sequence ref, sort by label (non-case-sensitive)</li>
* </ul>
*/
* <ul>
* <li>annotations with a reference to a sequence in the alignment are sorted
* on label (non-case-sensitive)</li>
- * <li>other annotations go 'at the end', with their mutual order unchanged</li>
+ * <li>other annotations go 'at the end', with their mutual order
+ * unchanged</li>
* <li>within the same label, sort by order of the related sequences</li>
* </ul>
*/
// cache 'alignment sequence position' for the annotations
saveSequenceIndices(alignmentAnnotations);
- Comparator<? super AlignmentAnnotation> comparator = getComparator(order);
+ Comparator<? super AlignmentAnnotation> comparator = getComparator(
+ order);
if (alignmentAnnotations != null)
{
{
if ((l != i) && (l != j))
{
- newdist[l] = ((distances.getValue(i, l) * noi) + (distances
- .getValue(j, l) * noj)) / (noi + noj);
+ newdist[l] = ((distances.getValue(i, l) * noi)
+ + (distances.getValue(j, l) * noj)) / (noi + noj);
}
else
{
* @param end
* end column position
*/
- public Conservation(String name, int threshold,
- List<SequenceI> sequences, int start, int end)
+ public Conservation(String name, int threshold, List<SequenceI> sequences,
+ int start, int end)
{
this.name = name;
this.threshold = threshold;
else
{
// JBPNote INFO level debug
- System.err
- .println("ERROR: calcSeqNum called with out of range sequence index for Alignment\n");
+ System.err.println(
+ "ERROR: calcSeqNum called with out of range sequence index for Alignment\n");
}
}
continue;
}
- char c = sequences[i].getCharAt(column); // gaps do not have upper/lower case
+ char c = sequences[i].getCharAt(column); // gaps do not have upper/lower
+ // case
if (Comparison.isGap((c)))
{
* @param endCol
* @param scoreMatrix
*/
- protected void findQuality(int startCol, int endCol, ScoreMatrix scoreMatrix)
+ protected void findQuality(int startCol, int endCol,
+ ScoreMatrix scoreMatrix)
{
quality = new Vector<Double>();
float vprop = value - min;
vprop /= max;
int consp = i - start;
- String conssym = (value > 0 && consp > -1 && consp < consSymbs.length) ? consSymbs[consp]
- : "";
+ String conssym = (value > 0 && consp > -1
+ && consp < consSymbs.length) ? consSymbs[consp] : "";
conservation.annotations[i] = new Annotation(String.valueOf(c),
- conssym, ' ', value, new Color(minR + (maxR * vprop), minG
- + (maxG * vprop), minB + (maxB * vprop)));
+ conssym, ' ', value, new Color(minR + (maxR * vprop),
+ minG + (maxG * vprop), minB + (maxB * vprop)));
}
// Quality calc
value = quality.elementAt(i).floatValue();
float vprop = value - qmin;
vprop /= qmax;
- quality2.annotations[i] = new Annotation(" ",
- String.valueOf(value), ' ', value, new Color(minR
- + (maxR * vprop), minG + (maxG * vprop), minB
- + (maxB * vprop)));
+ quality2.annotations[i] = new Annotation(" ", String.valueOf(value),
+ ' ', value, new Color(minR + (maxR * vprop),
+ minG + (maxG * vprop), minB + (maxB * vprop)));
}
}
}
char val = column < sequence.length ? sequence[column] : '-';
boolean hasConservation = val != '-' && val != '0';
int consp = column - start;
- String tip = (hasConservation && consp > -1 && consp < consSymbs.length) ? consSymbs[consp]
+ String tip = (hasConservation && consp > -1 && consp < consSymbs.length)
+ ? consSymbs[consp]
: "";
return tip;
}
*/
for (SequenceI rs : foundSeqs)
{
- DBRefEntry[] xrs = DBRefUtils
- .selectDbRefs(!fromDna, rs.getDBRefs());
+ DBRefEntry[] xrs = DBRefUtils.selectDbRefs(!fromDna,
+ rs.getDBRefs());
addXrefsToSources(xrs, sources);
}
}
dss = dss.getDatasetSequence();
}
boolean found = false;
- DBRefEntry[] xrfs = DBRefUtils
- .selectDbRefs(!fromDna, dss.getDBRefs());
+ DBRefEntry[] xrfs = DBRefUtils.selectDbRefs(!fromDna,
+ dss.getDBRefs());
// ENST & ENSP comes in to both Protein and nucleotide, so we need to
// filter them
// out later.
if (matchInDataset != null && xref.getMap().getTo() != null
&& matchInDataset != xref.getMap().getTo())
{
- System.err
- .println("Implementation problem (reopen JAL-2154): CrossRef.findInDataset seems to have recovered a different sequence than the one explicitly mapped for xref."
- + "Found:"
- + matchInDataset
- + "\nExpected:"
- + xref.getMap().getTo()
- + "\nFor xref:"
+ System.err.println(
+ "Implementation problem (reopen JAL-2154): CrossRef.findInDataset seems to have recovered a different sequence than the one explicitly mapped for xref."
+ + "Found:" + matchInDataset + "\nExpected:"
+ + xref.getMap().getTo() + "\nFor xref:"
+ xref);
}
/*matcher.findIdMatch(mappedTo);*/
}
else
{
- cf.addMap(matchInDataset, dss, xref.getMap().getMap()
- .getInverse(), xref.getMap().getMappedFromId());
+ cf.addMap(matchInDataset, dss,
+ xref.getMap().getMap().getInverse(),
+ xref.getMap().getMappedFromId());
}
}
if (fromDna)
{
// map is from dna seq to a protein product
- cf.addMap(dss, rsq, xref.getMap().getMap(), xref.getMap()
- .getMappedFromId());
+ cf.addMap(dss, rsq, xref.getMap().getMap(),
+ xref.getMap().getMappedFromId());
}
else
{
if (!found)
{
- SequenceI matchedSeq = matcher.findIdMatch(xref.getSource() + "|"
- + xref.getAccessionId());
+ SequenceI matchedSeq = matcher.findIdMatch(
+ xref.getSource() + "|" + xref.getAccessionId());
// if there was a match, check it's at least the right type of
// molecule!
if (matchedSeq != null && matchedSeq.isProtein() == fromDna)
{
ASequenceFetcher sftch = SequenceFetcherFactory.getSequenceFetcher();
SequenceI[] retrieved = null;
- SequenceI dss = seq.getDatasetSequence() == null ? seq : seq
- .getDatasetSequence();
+ SequenceI dss = seq.getDatasetSequence() == null ? seq
+ : seq.getDatasetSequence();
// first filter in case we are retrieving crossrefs that have already been
// retrieved. this happens for cases where a database record doesn't yield
// protein products for CDS
retrieved = sftch.getSequences(sourceRefs, !fromDna);
} catch (Exception e)
{
- System.err
- .println("Problem whilst retrieving cross references for Sequence : "
+ System.err.println(
+ "Problem whilst retrieving cross references for Sequence : "
+ seq.getName());
e.printStackTrace();
}
if (retrieved != null)
{
boolean addedXref = false;
- List<SequenceI> newDsSeqs = new ArrayList<SequenceI>(), doNotAdd = new ArrayList<SequenceI>();
+ List<SequenceI> newDsSeqs = new ArrayList<SequenceI>(),
+ doNotAdd = new ArrayList<SequenceI>();
for (SequenceI retrievedSequence : retrieved)
{
// dataset gets contaminated ccwith non-ds sequences. why ??!
// try: Ensembl -> Nuc->Ensembl, Nuc->Uniprot-->Protein->EMBL->
- SequenceI retrievedDss = retrievedSequence.getDatasetSequence() == null ? retrievedSequence
- : retrievedSequence.getDatasetSequence();
+ SequenceI retrievedDss = retrievedSequence
+ .getDatasetSequence() == null ? retrievedSequence
+ : retrievedSequence.getDatasetSequence();
addedXref |= importCrossRefSeq(cf, newDsSeqs, doNotAdd, dss,
retrievedDss);
}
{
// dataset gets contaminated ccwith non-ds sequences. why ??!
// try: Ensembl -> Nuc->Ensembl, Nuc->Uniprot-->Protein->EMBL->
- SequenceI retrievedDss = retrievedSequence.getDatasetSequence() == null ? retrievedSequence
- : retrievedSequence.getDatasetSequence();
+ SequenceI retrievedDss = retrievedSequence
+ .getDatasetSequence() == null ? retrievedSequence
+ : retrievedSequence.getDatasetSequence();
addedXref |= importCrossRefSeq(cf, newDsSeqs, doNotAdd, dss,
retrievedDss);
}
int sf = map.getMap().getToLowest();
int st = map.getMap().getToHighest();
SequenceI mappedrg = ms.getSubSequence(sf, st);
- if (mappedrg.getLength() > 0
- && ms.getSequenceAsString().equals(
- matched.getSequenceAsString()))
+ if (mappedrg.getLength() > 0 && ms.getSequenceAsString()
+ .equals(matched.getSequenceAsString()))
{
/*
* sequences were a match,
*/
for (DBRefEntry ref : toRefs)
{
- if (dbref.getSrcAccString().equals(
- ref.getSrcAccString()))
+ if (dbref.getSrcAccString()
+ .equals(ref.getSrcAccString()))
{
continue; // avoid overwriting the ref on source sequence
}
cf.addMap(retrievedSequence, map.getTo(), map.getMap());
} catch (Exception e)
{
- System.err
- .println("Exception when consolidating Mapped sequence set...");
+ System.err.println(
+ "Exception when consolidating Mapped sequence set...");
e.printStackTrace(System.err);
}
}
SequenceI mapsTo = xref.getMap().getTo();
String name = xref.getAccessionId();
String name2 = xref.getSource() + "|" + name;
- SequenceI dss = mapsTo.getDatasetSequence() == null ? mapsTo : mapsTo
- .getDatasetSequence();
+ SequenceI dss = mapsTo.getDatasetSequence() == null ? mapsTo
+ : mapsTo.getDatasetSequence();
// first check ds if ds is directly referenced
if (dataset.findIndex(dss) > -1)
{
for (SequenceI seq : dataset.getSequences())
{
// first check primary refs.
- List<DBRefEntry> match = DBRefUtils.searchRefs(seq.getPrimaryDBRefs()
- .toArray(new DBRefEntry[0]), template);
+ List<DBRefEntry> match = DBRefUtils.searchRefs(
+ seq.getPrimaryDBRefs().toArray(new DBRefEntry[0]), template);
if (match != null && match.size() == 1 && sameSequence(seq, dss))
{
return seq;
* returns sequences with a dbref to the matched accession id
* which we don't want
*/
- if (firstIdMatch == null
- && (name.equals(seq.getName()) || seq.getName().startsWith(
- name2)))
+ if (firstIdMatch == null && (name.equals(seq.getName())
+ || seq.getName().startsWith(name2)))
{
if (sameSequence(seq, dss))
{
MapList mapping = null;
SequenceI dsmapFrom = mapFrom.getDatasetSequence() == null ? mapFrom
: mapFrom.getDatasetSequence();
- SequenceI dsmapTo = mapTo.getDatasetSequence() == null ? mapTo : mapTo
- .getDatasetSequence();
+ SequenceI dsmapTo = mapTo.getDatasetSequence() == null ? mapTo
+ : mapTo.getDatasetSequence();
/*
* look for a reverse mapping, if found make its inverse.
* Note - we do this on dataset sequences only.
* @return true if matches were found.
*/
private boolean searchDatasetXrefs(boolean fromDna, SequenceI sequenceI,
- DBRefEntry[] lrfs, List<SequenceI> foundSeqs, AlignedCodonFrame cf)
+ DBRefEntry[] lrfs, List<SequenceI> foundSeqs,
+ AlignedCodonFrame cf)
{
boolean found = false;
if (lrfs == null)
// add in wildcards
xref.setVersion(null);
xref.setMap(null);
- found |= searchDataset(fromDna, sequenceI, xref, foundSeqs, cf, false);
+ found |= searchDataset(fromDna, sequenceI, xref, foundSeqs, cf,
+ false);
}
return found;
}
{
if (nxt.getDatasetSequence() != null)
{
- System.err
- .println("Implementation warning: CrossRef initialised with a dataset alignment with non-dataset sequences in it! ("
- + nxt.getDisplayId(true)
- + " has ds reference "
+ System.err.println(
+ "Implementation warning: CrossRef initialised with a dataset alignment with non-dataset sequences in it! ("
+ + nxt.getDisplayId(true) + " has ds reference "
+ nxt.getDatasetSequence().getDisplayId(true)
+ ")");
}
* @param ac2
* @return
*/
- public static final int compareCodonPos(AlignedCodon ac1, AlignedCodon ac2)
+ public static final int compareCodonPos(AlignedCodon ac1,
+ AlignedCodon ac2)
{
return comparator.compare(ac1, ac2);
// return jalview_2_8_2compare(ac1, ac2);
* @param ac2
* @return
*/
- private static int jalview_2_8_2compare(AlignedCodon ac1, AlignedCodon ac2)
+ private static int jalview_2_8_2compare(AlignedCodon ac1,
+ AlignedCodon ac2)
{
if (ac1 == null || ac2 == null || (ac1.equals(ac2)))
{
/*
* Filled up a reading frame...
*/
- AlignedCodon alignedCodon = new AlignedCodon(cdp[0], cdp[1], cdp[2]);
+ AlignedCodon alignedCodon = new AlignedCodon(cdp[0], cdp[1],
+ cdp[2]);
String aa = ResidueProperties.codonTranslate(new String(codon));
rf = 0;
final String gapString = String.valueOf(gapChar);
aa = gapString;
if (skipint == null)
{
- skipint = new int[] { alignedCodon.pos1, alignedCodon.pos3 /*
- * cdp[0],
- * cdp[2]
- */};
+ skipint = new int[] { alignedCodon.pos1,
+ alignedCodon.pos3 /*
+ * cdp[0],
+ * cdp[2]
+ */ };
}
skipint[1] = alignedCodon.pos3; // cdp[2];
}
}
if (vc + 2 < t.length)
{
- System.arraycopy(scontigs, vc + 2, t, vc, t.length
- - vc + 2);
+ System.arraycopy(scontigs, vc + 2, t, vc,
+ t.length - vc + 2);
}
scontigs = t;
}
}
else if (!alignedCodons[aspos].equals(alignedCodon))
{
- throw new IllegalStateException("Tried to coalign "
- + alignedCodons[aspos].toString() + " with "
- + alignedCodon.toString());
+ throw new IllegalStateException(
+ "Tried to coalign " + alignedCodons[aspos].toString()
+ + " with " + alignedCodon.toString());
}
if (aspos >= aaWidth)
{
{
for (SequenceFeature sf : sfs)
{
- fgstate = (featureGroups == null) ? null : featureGroups
- .get(sf.featureGroup);
+ fgstate = (featureGroups == null) ? null
+ : featureGroups.get(sf.featureGroup);
if ((featureTypes == null || featureTypes.containsKey(sf.getType()))
&& (fgstate == null || fgstate.booleanValue()))
{
{
resIndex = regex.matchedFrom();
- if ((selection != null && selection.getSize() > 0)
- && (resIndex + spaces.get(resIndex) < selection
- .getStartRes()))
+ if ((selection != null && selection.getSize() > 0) && (resIndex
+ + spaces.get(resIndex) < selection.getStartRes()))
{
continue;
}
int eres = seq.findPosition(regex.matchedTo() - 1
+ (spaces.get(regex.matchedTo() - 1)));
// only add result if not contained in previous result
- if (lastm == null
- || (lastm.getSequence() != seq || (!(lastm.getStart() <= sres && lastm
- .getEnd() >= eres))))
+ if (lastm == null || (lastm.getSequence() != seq
+ || (!(lastm.getStart() <= sres
+ && lastm.getEnd() >= eres))))
{
lastm = searchResults.addResult(seq, sres, eres);
}
i = 0;
for (String key : gps.keySet())
{
- SequenceGroup group = new SequenceGroup(gps.get(key), "Subseq: "
- + key, null, true, true, false, 0, width - 1);
+ SequenceGroup group = new SequenceGroup(gps.get(key),
+ "Subseq: " + key, null, true, true, false, 0, width - 1);
groups[i++] = group;
}
i = 0;
for (String key : gps.keySet())
{
- SequenceGroup group = new SequenceGroup(gps.get(key), "Subseq: "
- + key, null, true, true, false, 0, width - 1);
+ SequenceGroup group = new SequenceGroup(gps.get(key),
+ "Subseq: " + key, null, true, true, false, 0, width - 1);
groups[i++] = group;
}
* @param j
*/
@Override
- protected
- void findClusterDistance(int i, int j)
+ protected void findClusterDistance(int i, int j)
{
// New distances from cluster i to others
double[] newdist = new double[noseqs];
-
+
double ijDistance = distances.getValue(i, j);
for (int l = 0; l < noseqs; l++)
{
if ((l != i) && (l != j))
{
- newdist[l] = (distances.getValue(i, l) + distances.getValue(j, l) - ijDistance) / 2;
+ newdist[l] = (distances.getValue(i, l) + distances.getValue(j, l)
+ - ijDistance) / 2;
}
else
{
newdist[l] = 0;
}
}
-
+
for (int ii = 0; ii < noseqs; ii++)
{
distances.setValue(i, ii, newdist[ii]);
final private AlignmentView seqs;
private ScoreModelI scoreModel;
-
+
private SimilarityParamsI similarityParams;
public PCA(AlignmentView s, ScoreModelI sm, SimilarityParamsI options)
this.seqs = s;
this.similarityParams = options;
this.scoreModel = sm;
-
+
details.append("PCA calculation using " + sm.getName()
+ " sequence similarity matrix\n========\n\n");
}
q.printStackTrace();
details.append("\n*** Unexpected exception when performing PCA ***\n"
+ q.getLocalizedMessage());
- details.append("*** Matrices below may not be fully diagonalised. ***\n");
+ details.append(
+ "*** Matrices below may not be fully diagonalised. ***\n");
}
details.append(" --- New diagonalization matrix ---\n");
String ScoreDescriptions, String regex, boolean repeat)
{
return getScoresFromDescription(new String[] { ScoreName },
- new String[] { ScoreDescriptions }, regex, repeat);
+ new String[]
+ { ScoreDescriptions }, regex, repeat);
}
public int getScoresFromDescription(String[] ScoreNames,
* description string of each sequence
* @return total number of sequences that matched the regex
*/
- public int getScoresFromDescription(SequenceI[] seqs,
- String[] ScoreNames, String[] ScoreDescriptions, String regex,
- boolean repeat)
+ public int getScoresFromDescription(SequenceI[] seqs, String[] ScoreNames,
+ String[] ScoreDescriptions, String regex, boolean repeat)
{
int count = 0;
Regex pattern = new Regex(regex);
continue;
}
// add score to sequence annotation.
- AlignmentAnnotation an = new AlignmentAnnotation(ScoreNames[cols]
- + ((reps > 0) ? "_" + reps : ""),
+ AlignmentAnnotation an = new AlignmentAnnotation(
+ ScoreNames[cols] + ((reps > 0) ? "_" + reps : ""),
ScoreDescriptions[cols], null);
an.setScore(score);
System.out.println(seqs[i].getName() + " score: '"
*/
public static boolean isOpeningParenthesis(char c)
{
- return ('A' <= c && c <= 'Z' || c == '(' || c == '[' || c == '{' || c == '<');
+ return ('A' <= c && c <= 'Z' || c == '(' || c == '[' || c == '{'
+ || c == '<');
}
/**
*/
public static boolean isClosingParenthesis(char c)
{
- return ('a' <= c && c <= 'z' || c == ')' || c == ']' || c == '}' || c == '>');
+ return ('a' <= c && c <= 'z' || c == ')' || c == ']' || c == '}'
+ || c == '>');
}
/**
if (!stacks.containsKey(opening))
{
throw new WUSSParseException(MessageManager.formatMessage(
- "exception.mismatched_unseen_closing_char",
- new String[] { String.valueOf(base) }), i);
+ "exception.mismatched_unseen_closing_char", new String[]
+ { String.valueOf(base) }), i);
}
Stack<Integer> stack = stacks.get(opening);
{
// error whilst parsing i'th position. pass back
throw new WUSSParseException(MessageManager.formatMessage(
- "exception.mismatched_closing_char",
- new String[] { String.valueOf(base) }), i);
+ "exception.mismatched_closing_char", new String[]
+ { String.valueOf(base) }), i);
}
int temp = stack.pop();
* i (length of input string)
*/
throw new WUSSParseException(MessageManager.formatMessage(
- "exception.mismatched_opening_char",
- new String[] { String.valueOf(opening),
- String.valueOf(stack.pop()) }), i);
+ "exception.mismatched_opening_char", new String[]
+ { String.valueOf(opening), String.valueOf(stack.pop()) }),
+ i);
}
}
return pairs;
{
fact2 = tab[k + 1][j];
}
- tab[i][j] = Math.max(tab[i][j], basePairScore(seq, i, k)
- + fact1 + fact2);
+ tab[i][j] = Math.max(tab[i][j],
+ basePairScore(seq, i, k) + fact1 + fact2);
}
}
}
{
sq.setDescription(description);
}
- if ((seqds != null)
- && !(seqds.getName().equals("THISISAPLACEHOLDER") && seqds
- .getLength() == 0))
+ if ((seqds != null) && !(seqds.getName().equals("THISISAPLACEHOLDER")
+ && seqds.getLength() == 0))
{
if (sfeatures != null)
{
- System.err
- .println("Implementation error: setting dataset sequence for a sequence which has sequence features.\n\tDataset sequence features will not be visible.");
+ System.err.println(
+ "Implementation error: setting dataset sequence for a sequence which has sequence features.\n\tDataset sequence features will not be visible.");
}
sq.setDatasetSequence(seqds);
}
if (unmatched.size() > 0 && !quiet)
{
System.err.println("Did not find matches for :");
- for (Enumeration i = unmatched.elements(); i.hasMoreElements(); System.out
- .println(((SequenceI) i.nextElement()).getName()))
+ for (Enumeration i = unmatched.elements(); i
+ .hasMoreElements(); System.out
+ .println(((SequenceI) i.nextElement()).getName()))
{
;
}
names.put(new SeqIdName(cand.getName()), cand);
int q, w, candlen = cand.getName().length();
// keep the one with an id 'closer' to the given seqnam string
- if ((q = Math.abs(matchlen - namlen)) > (w = Math.abs(candlen
- - namlen))
- && candlen > matchlen)
+ if ((q = Math.abs(matchlen - namlen)) > (w = Math
+ .abs(candlen - namlen)) && candlen > matchlen)
{
best.clear();
match = cand;
@Override
public int hashCode()
{
- return ((id.length() >= 4) ? id.substring(0, 4).hashCode() : id
- .hashCode());
+ return ((id.length() >= 4) ? id.substring(0, 4).hashCode()
+ : id.hashCode());
}
@Override
{
if (id.length() > s.length())
{
- return id.startsWith(s) ? (WORD_SEP.indexOf(id.charAt(s.length())) > -1)
+ return id.startsWith(s)
+ ? (WORD_SEP.indexOf(id.charAt(s.length())) > -1)
: false;
}
else
{
- return s.startsWith(id) ? (s.equals(id) ? true : (WORD_SEP
- .indexOf(s.charAt(id.length())) > -1)) : false;
+ return s.startsWith(id)
+ ? (s.equals(id) ? true
+ : (WORD_SEP.indexOf(s.charAt(id.length())) > -1))
+ : false;
}
}
{
if (sequences[j] == null)
{
- System.err
- .println("WARNING: Consensus skipping null sequence - possible race condition.");
+ System.err.println(
+ "WARNING: Consensus skipping null sequence - possible race condition.");
continue;
}
if (profile)
{
// TODO 1-dim array with jsize in [0], nongapped in [1]; or Pojo
- residueHash.put(PROFILE, new int[][] { values,
- new int[] { jSize, (jSize - values['-']) } });
+ residueHash.put(PROFILE,
+ new int[][]
+ { values, new int[] { jSize, (jSize - values['-']) } });
residueHash.put(PAIRPROFILE, pairs);
}
{
if (canonicalOrWobblePairCount >= otherPairCount)
{
- maxResidue = (canonicalOrWobblePairCount - canonical) < canonical ? "("
+ maxResidue = (canonicalOrWobblePairCount - canonical) < canonical
+ ? "("
: "[";
}
else
residueHash = new Hashtable();
if (profile)
{
- residueHash.put(PROFILE, new int[][] { values,
- new int[] { jSize, (jSize - values['-']) } });
+ residueHash.put(PROFILE,
+ new int[][]
+ { values, new int[] { jSize, (jSize - values['-']) } });
residueHash.put(PAIRPROFILE, pairs);
}
int valuesCount = 0;
rtnval[1] = 0;
int offset = 2;
- final int divisor = profile[1][ignoreGapsInConsensusCalculation ? 1 : 0];
+ final int divisor = profile[1][ignoreGapsInConsensusCalculation ? 1
+ : 0];
for (int c = 624; c > 0; c--)
{
if (vl[c] > 0)
{
start = av.getSelectionGroup().getStartRes();
end = av.getSelectionGroup().getEndRes() + 1;
- this.sequences = av.getSelectionGroup().getSequencesInOrder(
- av.getAlignment());
+ this.sequences = av.getSelectionGroup()
+ .getSequencesInOrder(av.getAlignment());
}
init(seqStrings, start, end);
{
return maxheight;
}
-
+
if ((nd.left() == null) && (nd.right() == null))
{
nd.height = ((SequenceNode) nd.parent()).height + nd.dist;
-
+
if (nd.height > maxheight)
{
return nd.height;
maxheight = 0;
nd.height = (float) 0.0;
}
-
+
maxheight = findHeight((SequenceNode) (nd.left()));
maxheight = findHeight((SequenceNode) (nd.right()));
}
-
+
return maxheight;
}
{
// if (_lycount<_lylimit)
// {
- // System.err.println("Warning: depth of _recount greater than number of nodes.");
+ // System.err.println("Warning: depth of _recount greater than number of
+ // nodes.");
// }
if (nd == null)
{
return;
}
// _lycount++;
-
+
if ((nd.left() != null) && (nd.right() != null))
{
-
+
_reCount((SequenceNode) nd.left());
_reCount((SequenceNode) nd.right());
-
+
SequenceNode l = (SequenceNode) nd.left();
SequenceNode r = (SequenceNode) nd.right();
-
+
nd.count = l.count + r.count;
nd.ycount = (l.ycount + r.ycount) / 2;
}
while (noClus > 2)
{
findMinDistance();
-
+
joinClusters(mini, minj);
-
+
noClus--;
}
-
+
int rightChild = done.nextClearBit(0);
int leftChild = done.nextClearBit(rightChild + 1);
-
+
joinClusters(leftChild, rightChild);
top = (node.elementAt(leftChild));
-
+
reCount(top);
findHeight(top);
findMaxDist(top);
protected void computeTree(ScoreModelI sm, SimilarityParamsI scoreOptions)
{
distances = sm.findDistances(seqData, scoreOptions);
-
+
makeLeaves();
-
+
noClus = clusters.size();
-
+
cluster();
}
{
return;
}
-
+
if ((nd.left() == null) && (nd.right() == null))
{
double dist = nd.dist;
-
+
if (dist > maxDistValue)
{
maxdist = nd;
protected double findr(int i, int j)
{
double tmp = 1;
-
+
for (int k = 0; k < noseqs; k++)
{
if ((k != i) && (k != j) && (!done.get(k)))
tmp = tmp + distances.getValue(i, k);
}
}
-
+
if (noClus > 2)
{
tmp = tmp / (noClus - 2);
}
-
+
return tmp;
}
sdata.addOperation(CigarArray.M, end - start + 1);
this.seqData = new AlignmentView(sdata, start);
}
-
+
/*
* count the non-null sequences
*/
noseqs = 0;
-
+
done = new BitSet();
-
+
for (SequenceI seq : sequences)
{
if (seq != null)
void joinClusters(final int i, final int j)
{
double dist = distances.getValue(i, j);
-
+
ri = findr(i, j);
rj = findr(j, i);
-
+
findClusterDistance(i, j);
-
+
SequenceNode sn = new SequenceNode();
-
+
sn.setLeft((node.elementAt(i)));
sn.setRight((node.elementAt(j)));
-
+
SequenceNode tmpi = (node.elementAt(i));
SequenceNode tmpj = (node.elementAt(j));
-
+
findNewDistances(tmpi, tmpj, dist);
-
+
tmpi.setParent(sn);
tmpj.setParent(sn);
-
+
node.setElementAt(sn, i);
-
+
/*
* move the members of cluster(j) to cluster(i)
* and mark cluster j as out of the game
void makeLeaves()
{
clusters = new Vector<BitSet>();
-
+
for (int i = 0; i < noseqs; i++)
{
SequenceNode sn = new SequenceNode();
-
+
sn.setElement(sequences[i]);
sn.setName(sequences[i].getName());
node.addElement(sn);
* @param treefile
* NewickFile
*/
- public TreeModel(SequenceI[] seqs, AlignmentView odata, NewickFile treefile)
+ public TreeModel(SequenceI[] seqs, AlignmentView odata,
+ NewickFile treefile)
{
- this(seqs, treefile.getTree(), treefile.HasDistances(), treefile
- .HasBootstrap(), treefile.HasRootDistance());
+ this(seqs, treefile.getTree(), treefile.HasDistances(),
+ treefile.HasBootstrap(), treefile.HasRootDistance());
seqData = odata;
associateLeavesToSequences(seqs);
*/
public TreeModel(TreeBuilder tree)
{
- this(tree.getSequences(), tree.getTopNode(), tree.hasDistances(), tree
- .hasBootstrap(), tree.hasRootDistance());
+ this(tree.getSequences(), tree.getTopNode(), tree.hasDistances(),
+ tree.hasBootstrap(), tree.hasRootDistance());
seqData = tree.getOriginalData();
}
{
NewickFile fout = new NewickFile(getTopNode());
- return fout.print(hasBootstrap(), hasDistances(),
- hasRootDistance()); // output all data available for tree
+ return fout.print(hasBootstrap(), hasDistances(), hasRootDistance()); // output
+ // all
+ // data
+ // available
+ // for
+ // tree
}
/**
if (!leaf.isPlaceholder())
{
// Construct a new placeholder sequence object for this leaf
- leaf.setElement(new Sequence(leaf.getName(),
- "THISISAPLACEHLDER"));
+ leaf.setElement(
+ new Sequence(leaf.getName(), "THISISAPLACEHLDER"));
}
leaf.setPlaceholder(true);
System.out.println(" name = " + ((SequenceI) nd.element()).getName());
}
- System.out.println(" dist = " + nd.dist + " " + nd.count + " "
- + nd.height);
+ System.out.println(
+ " dist = " + nd.dist + " " + nd.count + " " + nd.height);
}
/**
{
// if (_lycount<_lylimit)
// {
- // System.err.println("Warning: depth of _recount greater than number of nodes.");
+ // System.err.println("Warning: depth of _recount greater than number of
+ // nodes.");
// }
if (nd == null)
{
public void applyToNodes(NodeTransformI nodeTransformI)
{
for (Enumeration<SequenceNode> nodes = node.elements(); nodes
- .hasMoreElements(); nodeTransformI.transform(nodes
- .nextElement()))
+ .hasMoreElements(); nodeTransformI
+ .transform(nodes.nextElement()))
{
;
}
/*
* first record feature types in this column for each sequence
*/
- Map<SeqCigar, Set<String>> sfap = findFeatureTypesAtColumn(
- seqs, cpos);
+ Map<SeqCigar, Set<String>> sfap = findFeatureTypesAtColumn(seqs,
+ cpos);
/*
* count feature types on either i'th or j'th sequence but not both
* Instances of this class are immutable and thread-safe, so the same object is
* returned from calls to getInstance().
*/
-public class PIDModel extends SimilarityScoreModel implements
- PairwiseScoreModelI
+public class PIDModel extends SimilarityScoreModel
+ implements PairwiseScoreModelI
{
private static final String NAME = "PID";
* symbols. Instances of this class are immutable and thread-safe, so the same
* object is returned from calls to getInstance().
*/
-public class ScoreMatrix extends SimilarityScoreModel implements
- PairwiseScoreModelI
+public class ScoreMatrix extends SimilarityScoreModel
+ implements PairwiseScoreModelI
{
private static final char GAP_CHARACTER = Comparison.GAP_DASH;
private float minValue;
private float maxValue;
-
+
/**
* Constructor given a name, symbol alphabet, and matrix of scores for pairs
* of symbols. The matrix should be square and of the same size as the
* @param values
* Pairwise scores indexed according to the symbol alphabet
*/
- public ScoreMatrix(String theName, String theDescription,
- char[] alphabet, float[][] values)
+ public ScoreMatrix(String theName, String theDescription, char[] alphabet,
+ float[][] values)
{
if (alphabet.length != values.length)
{
* @param params
* @return
*/
- protected MatrixI findSimilarities(String[] seqs, SimilarityParamsI params)
+ protected MatrixI findSimilarities(String[] seqs,
+ SimilarityParamsI params)
{
double[][] values = new double[seqs.length][];
for (int row = 0; row < seqs.length; row++)
/*
* delegate parsing to ScoreMatrixFile
*/
- FileParse fp = new FileParse(resourcePath, DataSourceType.CLASSLOADER);
+ FileParse fp = new FileParse(resourcePath,
+ DataSourceType.CLASSLOADER);
ScoreMatrix sm = new ScoreMatrixFile(fp).parseMatrix();
registerScoreModel(sm);
return sm;
} catch (IOException e)
{
- System.err.println("Error reading " + resourcePath + ": "
- + e.getMessage());
+ System.err.println(
+ "Error reading " + resourcePath + ": " + e.getMessage());
}
return null;
}
* Based on Jalview's Comparison.PID method, which includes gaps and counts
* them as matching; it counts over the length of the shorter sequence
*/
- public static final SimilarityParamsI Jalview = new SimilarityParams(
- true, true, true, true);
+ public static final SimilarityParamsI Jalview = new SimilarityParams(true,
+ true, true, true);
/**
* 'SeqSpace' mode PCA calculation includes gaps but does not count them as
public MatrixI findSimilarities(AlignmentView seqData,
SimilarityParamsI options)
{
- SequenceI[] sequenceString = seqData.getVisibleAlignment(
- Comparison.GAP_SPACE).getSequencesArray();
+ SequenceI[] sequenceString = seqData
+ .getVisibleAlignment(Comparison.GAP_SPACE).getSequencesArray();
int noseqs = sequenceString.length;
double[][] distances = new double[noseqs][noseqs];
public boolean updateFrom(DBRefEntryI otherEntry);
/**
- * Answers true if the ref looks like a primary (direct) database reference. <br>
+ * Answers true if the ref looks like a primary (direct) database reference.
+ * <br>
* The only way a dbref's mappings can be fully verified is via the local
* sequence frame, so rather than use isPrimaryCandidate directly, please use
* SequenceI.getPrimaryDbRefs(). <br>
* @param options
* @return
*/
- MatrixI findSimilarities(AlignmentView seqData, SimilarityParamsI options);
+ MatrixI findSimilarities(AlignmentView seqData,
+ SimilarityParamsI options);
/**
* Returns a score model object configured for the given alignment view.
import java.util.TreeMap;
import java.util.Vector;
-public class APopupMenu extends java.awt.PopupMenu implements
- ActionListener, ItemListener
+public class APopupMenu extends java.awt.PopupMenu
+ implements ActionListener, ItemListener
{
Menu groupMenu = new Menu();
purinePyrimidineColour.setEnabled(false);
nucleotideColour.setEnabled(false);
}
- editGroupName.setLabel(MessageManager.formatMessage(
- "label.name_param", new Object[] { sg.getName() }));
+ editGroupName.setLabel(
+ MessageManager.formatMessage("label.name_param", new Object[]
+ { sg.getName() }));
showText.setState(sg.getDisplayText());
showColourText.setState(sg.getColourText());
showBoxes.setState(sg.getDisplayBoxes());
seqMenu.setLabel(seq.getName());
if (seq == ap.av.getAlignment().getSeqrep())
{
- makeReferenceSeq.setLabel(MessageManager
- .getString("action.unmark_as_reference"));// Unmark
- // representative");
+ makeReferenceSeq.setLabel(
+ MessageManager.getString("action.unmark_as_reference"));// Unmark
+ // representative");
}
else
{
- makeReferenceSeq.setLabel(MessageManager
- .getString("action.set_as_reference")); // );
+ makeReferenceSeq.setLabel(
+ MessageManager.getString("action.set_as_reference")); // );
}
- repGroup.setLabel(MessageManager.formatMessage(
- "label.represent_group_with", new Object[] { seq.getName() }));
+ repGroup.setLabel(MessageManager
+ .formatMessage("label.represent_group_with", new Object[]
+ { seq.getName() }));
}
else
{
/*
* First for the currently selected sequence (if there is one):
*/
- final List<SequenceI> selectedSequence = (seq == null ? Collections
- .<SequenceI> emptyList() : Arrays.asList(seq));
+ final List<SequenceI> selectedSequence = (seq == null
+ ? Collections.<SequenceI> emptyList()
+ : Arrays.asList(seq));
buildAnnotationTypesMenus(seqShowAnnotationsMenu,
seqHideAnnotationsMenu, selectedSequence);
configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
/*
* and repeat for the current selection group (if there is one):
*/
- final List<SequenceI> selectedGroup = (ap.av.getSelectionGroup() == null ? Collections
- .<SequenceI> emptyList() : ap.av.getSelectionGroup()
- .getSequences());
+ final List<SequenceI> selectedGroup = (ap.av.getSelectionGroup() == null
+ ? Collections.<SequenceI> emptyList()
+ : ap.av.getSelectionGroup().getSequences());
buildAnnotationTypesMenus(groupShowAnnotationsMenu,
groupHideAnnotationsMenu, selectedGroup);
configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
SortedMap<String, String> tipEntries = new TreeMap<String, String>();
final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
AlignmentI al = this.ap.av.getAlignment();
- AlignmentUtils.findAddableReferenceAnnotations(forSequences,
- tipEntries, candidates, al);
+ AlignmentUtils.findAddableReferenceAnnotations(forSequences, tipEntries,
+ candidates, al);
if (!candidates.isEmpty())
{
StringBuilder tooltip = new StringBuilder(64);
seq = sg.getSequenceAt(0);
}
- EditNameDialog dialog = new EditNameDialog(seq.getSequenceAsString(
- sg.getStartRes(), sg.getEndRes() + 1), null,
- "Edit Sequence ", null,
+ EditNameDialog dialog = new EditNameDialog(
+ seq.getSequenceAsString(sg.getStartRes(),
+ sg.getEndRes() + 1),
+ null, "Edit Sequence ", null,
ap.alignFrame, "Edit Sequence", 500, 100, true);
{
EditCommand editCommand = new EditCommand(
MessageManager.getString("label.edit_sequences"),
- Action.REPLACE, dialog.getName().replace(' ',
- ap.av.getGapCharacter()),
+ Action.REPLACE,
+ dialog.getName().replace(' ', ap.av.getGapCharacter()),
sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
sg.getStartRes(), sg.getEndRes() + 1,
ap.av.getAlignment());
ap.alignFrame.addHistoryItem(editCommand);
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
- .getSequences());
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
}
}
}
ap.alignFrame.addHistoryItem(caseCommand);
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
- .getSequences());
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
}
}
Frame frame = new Frame();
frame.add(cap);
- JalviewLite.addFrame(frame, MessageManager.formatMessage(
- "label.selection_output_command",
- new Object[] { e.getActionCommand() }), 600, 500);
+ JalviewLite.addFrame(frame, MessageManager
+ .formatMessage("label.selection_output_command", new Object[]
+ { e.getActionCommand() }), 600, 500);
// JBPNote: getSelectionAsNewSequence behaviour has changed - this method
// now returns a full copy of sequence data
// TODO consider using getSequenceSelection instead here
- FileFormatI fileFormat = FileFormats.getInstance().forName(
- e.getActionCommand());
+ FileFormatI fileFormat = FileFormats.getInstance()
+ .forName(e.getActionCommand());
cap.setText(new AppletFormatAdapter().formatSequences(fileFormat,
ap.av.getShowJVSuffix(), ap, true));
StringBuilder contents = new StringBuilder(128);
for (SequenceI seq : sequences)
{
- contents.append(MessageManager.formatMessage(
- "label.annotation_for_displayid",
- new Object[] { seq.getDisplayId(true) }));
+ contents.append(MessageManager
+ .formatMessage("label.annotation_for_displayid", new Object[]
+ { seq.getDisplayId(true) }));
new SequenceAnnotationReport(null).createSequenceAnnotationReport(
- contents,
- seq,
- true,
- true,
- (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr
- .getMinMax() : null);
+ contents, seq, true, true,
+ (ap.seqPanel.seqCanvas.fr != null)
+ ? ap.seqPanel.seqCanvas.fr.getMinMax()
+ : null);
contents.append("</p>");
}
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Sequence Details for "
- + (sequences.length == 1 ? sequences[0].getDisplayId(true)
- : "Selection"), 600, 500);
- cap.setText(MessageManager.formatMessage("label.html_content",
- new Object[] { contents.toString() }));
+ jalview.bin.JalviewLite.addFrame(frame,
+ "Sequence Details for " + (sequences.length == 1
+ ? sequences[0].getDisplayId(true)
+ : "Selection"),
+ 600, 500);
+ cap.setText(
+ MessageManager.formatMessage("label.html_content", new Object[]
+ { contents.toString() }));
}
void editName()
}
else
{
- new MCview.AppletPDBViewer(entry, new SequenceI[] { seq }, null,
- ap, DataSourceType.URL);
+ new MCview.AppletPDBViewer(entry, new SequenceI[] { seq }, null, ap,
+ DataSourceType.URL);
}
}
else
{
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true,
+ ap.alignFrame);
cap.setText(MessageManager.getString("label.paste_pdb_file"));
cap.setPDBImport(seq);
Frame frame = new Frame();
frame.add(cap);
JalviewLite.addFrame(frame, MessageManager.formatMessage(
- "label.paste_pdb_file_for_sequence",
- new Object[] { seq.getName() }), 400, 300);
+ "label.paste_pdb_file_for_sequence", new Object[]
+ { seq.getName() }), 400, 300);
}
}
sequenceFeature.addActionListener(this);
editGroupName.addActionListener(this);
- unGroupMenuItem.setLabel(MessageManager
- .getString("action.remove_group"));
+ unGroupMenuItem
+ .setLabel(MessageManager.getString("action.remove_group"));
unGroupMenuItem.addActionListener(this);
- createGroupMenuItem.setLabel(MessageManager
- .getString("action.create_group"));
+ createGroupMenuItem
+ .setLabel(MessageManager.getString("action.create_group"));
createGroupMenuItem.addActionListener(this);
modifyPID.setEnabled(abovePIDColour.getState());
sequenceName.addActionListener(this);
sequenceDetails.addActionListener(this);
selSeqDetails.addActionListener(this);
- displayNonconserved.setLabel(MessageManager
- .getString("label.show_non_conserved"));
+ displayNonconserved
+ .setLabel(MessageManager.getString("label.show_non_conserved"));
displayNonconserved.setState(false);
displayNonconserved.addItemListener(this);
showText.setLabel(MessageManager.getString("action.text"));
seqMenu.setLabel(MessageManager.getString("label.sequence"));
pdb.setLabel(MessageManager.getString("label.view_pdb_structure"));
hideSeqs.setLabel(MessageManager.getString("action.hide_sequences"));
- repGroup.setLabel(MessageManager.formatMessage(
- "label.represent_group_with", new Object[] { "" }));
+ repGroup.setLabel(MessageManager
+ .formatMessage("label.represent_group_with", new Object[]
+ { "" }));
revealAll.setLabel(MessageManager.getString("action.reveal_all"));
revealSeq.setLabel(MessageManager.getString("action.reveal_sequences"));
menu1.setLabel(MessageManager.getString("label.group:"));
/*
* setName allows setSelectedColour to do its thing
*/
- clustalColour.setLabel(MessageManager
- .getString("label.colourScheme_clustal"));
+ clustalColour.setLabel(
+ MessageManager.getString("label.colourScheme_clustal"));
clustalColour.setName(JalviewColourScheme.Clustal.toString());
clustalColour.addItemListener(this);
- BLOSUM62Colour.setLabel(MessageManager
- .getString("label.colourScheme_blosum62"));
+ BLOSUM62Colour.setLabel(
+ MessageManager.getString("label.colourScheme_blosum62"));
BLOSUM62Colour.setName(JalviewColourScheme.Blosum62.toString());
BLOSUM62Colour.addItemListener(this);
- PIDColour.setLabel(MessageManager
- .getString("label.colourScheme_%_identity"));
+ PIDColour.setLabel(
+ MessageManager.getString("label.colourScheme_%_identity"));
PIDColour.setName(JalviewColourScheme.PID.toString());
PIDColour.addItemListener(this);
- zappoColour.setLabel(MessageManager
- .getString("label.colourScheme_zappo"));
+ zappoColour
+ .setLabel(MessageManager.getString("label.colourScheme_zappo"));
zappoColour.setName(JalviewColourScheme.Zappo.toString());
zappoColour.addItemListener(this);
- taylorColour.setLabel(MessageManager
- .getString("label.colourScheme_taylor"));
+ taylorColour.setLabel(
+ MessageManager.getString("label.colourScheme_taylor"));
taylorColour.setName(JalviewColourScheme.Taylor.toString());
taylorColour.addItemListener(this);
- hydrophobicityColour.setLabel(MessageManager
- .getString("label.colourScheme_hydrophobic"));
+ hydrophobicityColour.setLabel(
+ MessageManager.getString("label.colourScheme_hydrophobic"));
hydrophobicityColour
.setName(JalviewColourScheme.Hydrophobic.toString());
hydrophobicityColour.addItemListener(this);
.getString("label.colourScheme_strand_propensity"));
strandColour.setName(JalviewColourScheme.Strand.toString());
strandColour.addItemListener(this);
- turnColour.setLabel(MessageManager
- .getString("label.colourScheme_turn_propensity"));
+ turnColour.setLabel(
+ MessageManager.getString("label.colourScheme_turn_propensity"));
turnColour.setName(JalviewColourScheme.Turn.toString());
turnColour.addItemListener(this);
- buriedColour.setLabel(MessageManager
- .getString("label.colourScheme_buried_index"));
+ buriedColour.setLabel(
+ MessageManager.getString("label.colourScheme_buried_index"));
buriedColour.setName(JalviewColourScheme.Buried.toString());
buriedColour.addItemListener(this);
- nucleotideColour.setLabel(MessageManager
- .getString("label.colourScheme_nucleotide"));
+ nucleotideColour.setLabel(
+ MessageManager.getString("label.colourScheme_nucleotide"));
nucleotideColour.setName(JalviewColourScheme.Nucleotide.toString());
nucleotideColour.addItemListener(this);
purinePyrimidineColour.setLabel(MessageManager
.getString("label.colourScheme_purine/pyrimidine"));
- purinePyrimidineColour.setName(JalviewColourScheme.PurinePyrimidine
- .toString());
+ purinePyrimidineColour
+ .setName(JalviewColourScheme.PurinePyrimidine.toString());
purinePyrimidineColour.addItemListener(this);
- userDefinedColour.setLabel(MessageManager
- .getString("action.user_defined"));
+ userDefinedColour
+ .setLabel(MessageManager.getString("action.user_defined"));
userDefinedColour.addActionListener(this);
- abovePIDColour.setLabel(MessageManager
- .getString("label.above_identity_threshold"));
+ abovePIDColour.setLabel(
+ MessageManager.getString("label.above_identity_threshold"));
abovePIDColour.addItemListener(this);
- modifyPID.setLabel(MessageManager
- .getString("label.modify_identity_threshold"));
+ modifyPID.setLabel(
+ MessageManager.getString("label.modify_identity_threshold"));
modifyPID.addActionListener(this);
- conservationColour.setLabel(MessageManager
- .getString("action.by_conservation"));
+ conservationColour
+ .setLabel(MessageManager.getString("action.by_conservation"));
conservationColour.addItemListener(this);
modifyConservation.setLabel(MessageManager
.getString("label.modify_conservation_threshold"));
protected void clustalColour_actionPerformed()
{
SequenceGroup sg = getGroup();
- sg.cs = new ResidueShader(new ClustalxColourScheme(sg,
- ap.av.getHiddenRepSequences()));
+ sg.cs = new ResidueShader(
+ new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences()));
refresh();
}
public void purinePyrimidineColour_actionPerformed()
{
- getGroup().cs = new ResidueShader(
- new PurinePyrimidineColourScheme());
+ getGroup().cs = new ResidueShader(new PurinePyrimidineColourScheme());
refresh();
}
if (abovePIDColour.getState())
{
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
- .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
- int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
- .getName());
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(ap.av.getHiddenRepSequences()), 0,
+ ap.av.getAlignment().getWidth()));
+ int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
+ getGroup().getName());
sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
{
SequenceGroup sg = getGroup();
sg.cs = new ResidueShader(new PIDColourScheme());
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
- .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(ap.av.getHiddenRepSequences()), 0,
+ ap.av.getAlignment().getWidth()));
refresh();
}
sg.cs = new ResidueShader(new Blosum62ColourScheme());
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
- .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(ap.av.getHiddenRepSequences()), 0,
+ ap.av.getAlignment().getWidth()));
refresh();
}
if (conservationColour.getState())
{
Conservation conservation = Conservation.calculateConservation(
- "Group", sg
- .getSequences(ap.av.getHiddenRepSequences()), 0, ap.av
- .getAlignment().getWidth(), false, ap.av.getConsPercGaps(),
- false);
+ "Group", sg.getSequences(ap.av.getHiddenRepSequences()), 0,
+ ap.av.getAlignment().getWidth(), false,
+ ap.av.getConsPercGaps(), false);
sg.getGroupColourScheme().setConservation(conservation);
SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
SliderPanel.showConservationSlider();
showMenu.removeAll();
hideMenu.removeAll();
- final List<String> all = Arrays.asList(new String[] { MessageManager
- .getString("label.all") });
- addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
+ final List<String> all = Arrays
+ .asList(new String[]
+ { MessageManager.getString("label.all") });
+ addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true,
+ true);
addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
false);
showMenu.addSeparator();
}
public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
- HiddenColumns hidden, JalviewLite applet,
- String title, boolean embedded)
+ HiddenColumns hidden, JalviewLite applet, String title,
+ boolean embedded)
{
this(al, hiddenSeqs, hidden, applet, title, embedded, true);
}
public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
- HiddenColumns hidden, JalviewLite applet,
- String title, boolean embedded, boolean addToDisplay)
+ HiddenColumns hidden, JalviewLite applet, String title,
+ boolean embedded, boolean addToDisplay)
{
if (applet != null)
{
{
Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
.getFeatureRenderer().getFeatureColours();
- boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
- "relaxedidmatch", false);
+ boolean relaxedIdMatching = viewport.applet
+ .getDefaultParameter("relaxedidmatch", false);
featuresFile = new FeaturesFile(file, sourceType).parse(
viewport.getAlignment(), colours, true, relaxedIdMatching);
} catch (Exception ex)
ViewportRanges ranges = viewport.getRanges();
if (viewport.cursorMode
- && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
- .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
- .getKeyCode() <= KeyEvent.VK_NUMPAD9))
+ && ((evt.getKeyCode() >= KeyEvent.VK_0
+ && evt.getKeyCode() <= KeyEvent.VK_9)
+ || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
+ && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
&& Character.isDigit(evt.getKeyChar()))
{
alignPanel.seqPanel.numberPressed(evt.getKeyChar());
case KeyEvent.VK_F2:
viewport.cursorMode = !viewport.cursorMode;
- statusBar.setText(MessageManager.formatMessage(
- "label.keyboard_editing_mode",
- new String[] { (viewport.cursorMode ? "on" : "off") }));
+ statusBar.setText(MessageManager
+ .formatMessage("label.keyboard_editing_mode", new String[]
+ { (viewport.cursorMode ? "on" : "off") }));
if (viewport.cursorMode)
{
alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes();
// Hide everything by the current selection - this is a hack - we do the
// invert and then hide
// first check that there will be visible columns after the invert.
- if (viewport.hasSelectedColumns()
- || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
- .getEndRes()))
+ if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
+ && sg.getStartRes() <= sg.getEndRes()))
{
// now invert the sequence set, if required - empty selection implies
// that no hiding is required.
{
boolean newState = sortAnnBySequence.getState();
sortAnnByLabel.setState(false);
- setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
- : SequenceAnnotationOrder.NONE);
+ setAnnotationSortOrder(
+ newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
+ : SequenceAnnotationOrder.NONE);
setViewportAnnotationOrder();
}
else if (source == sortAnnByLabel)
{
boolean newState = sortAnnByLabel.getState();
sortAnnBySequence.setState(false);
- setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
- : SequenceAnnotationOrder.NONE);
+ setAnnotationSortOrder(
+ newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
+ : SequenceAnnotationOrder.NONE);
setViewportAnnotationOrder();
}
else if (source == showAutoFirst)
cap.setText(contents.toString());
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
- "label.alignment_properties", new String[] { getTitle() }),
- 400, 250);
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager
+ .formatMessage("label.alignment_properties", new String[]
+ { getTitle() }), 400, 250);
}
else if (source == overviewMenuItem)
{
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
Frame frame = new Frame();
frame.add(cap);
- JalviewLite.addFrame(frame, MessageManager.formatMessage(
- "label.alignment_output_command",
- new Object[] { e.getActionCommand() }), 600, 500);
-
- FileFormatI fileFormat = FileFormats.getInstance().forName(
- e.getActionCommand());
- cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
- fileFormat, viewport.getAlignment(),
- viewport.getShowJVSuffix()));
+ JalviewLite.addFrame(frame, MessageManager
+ .formatMessage("label.alignment_output_command", new Object[]
+ { e.getActionCommand() }), 600, 500);
+
+ FileFormatI fileFormat = FileFormats.getInstance()
+ .forName(e.getActionCommand());
+ cap.setText(
+ new AppletFormatAdapter(alignPanel).formatSequences(fileFormat,
+ viewport.getAlignment(), viewport.getShowJVSuffix()));
}
public void loadAnnotations()
FeaturesFile formatter = new FeaturesFile();
if (format.equalsIgnoreCase("Jalview"))
{
- features = formatter.printJalviewFormat(viewport.getAlignment()
- .getSequencesArray(), getDisplayedFeatureCols());
+ features = formatter.printJalviewFormat(
+ viewport.getAlignment().getSequencesArray(),
+ getDisplayedFeatureCols());
}
else
{
- features = formatter.printGffFormat(viewport.getAlignment()
- .getSequencesArray(), getDisplayedFeatureCols());
+ features = formatter.printGffFormat(
+ viewport.getAlignment().getSequencesArray(),
+ getDisplayedFeatureCols());
}
if (displayTextbox)
: "?";
url.append(firstSep);
- url.append("open="
- + appendProtocol(viewport.applet.getParameter("file")));
+ url.append(
+ "open=" + appendProtocol(viewport.applet.getParameter("file")));
if (viewport.applet.getParameter("features") != null)
{
if (viewport.applet.getParameter("annotations") != null)
{
url.append("&annotations=");
- url.append(appendProtocol(viewport.applet.getParameter("annotations")));
+ url.append(
+ appendProtocol(viewport.applet.getParameter("annotations")));
}
if (viewport.applet.getParameter("jnetfile") != null
|| viewport.applet.getParameter("jpredfile") != null)
{
url.append("&annotations=");
- url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet
- .getParameter("jnetfile") : viewport.applet
- .getParameter("jpredfile")));
+ url.append(appendProtocol(
+ viewport.applet.getParameter("jnetfile") != null
+ ? viewport.applet.getParameter("jnetfile")
+ : viewport.applet.getParameter("jpredfile")));
}
if (viewport.applet.getParameter("defaultColour") != null)
{
- url.append("&colour="
- + removeWhiteSpace(viewport.applet
- .getParameter("defaultColour")));
+ url.append("&colour=" + removeWhiteSpace(
+ viewport.applet.getParameter("defaultColour")));
}
if (viewport.applet.getParameter("userDefinedColour") != null)
{
- url.append("&colour="
- + removeWhiteSpace(viewport.applet
- .getParameter("userDefinedColour")));
+ url.append("&colour=" + removeWhiteSpace(
+ viewport.applet.getParameter("userDefinedColour")));
}
if (viewport.applet.getParameter("tree") != null)
{
{
undoMenuItem.setEnabled(true);
CommandI command = viewport.getHistoryList().peek();
- undoMenuItem.setLabel(MessageManager.formatMessage(
- "label.undo_command",
- new Object[] { command.getDescription() }));
+ undoMenuItem.setLabel(MessageManager
+ .formatMessage("label.undo_command", new Object[]
+ { command.getDescription() }));
}
else
{
redoMenuItem.setEnabled(true);
CommandI command = viewport.getRedoList().peek();
- redoMenuItem.setLabel(MessageManager.formatMessage(
- "label.redo_command",
- new Object[] { command.getDescription() }));
+ redoMenuItem.setLabel(MessageManager
+ .formatMessage("label.redo_command", new Object[]
+ { command.getDescription() }));
}
else
{
// viewport.getColumnSelection().getHiddenColumns()
// != null;
updateEditMenuBar();
- originalSource.firePropertyChange("alignment", null, originalSource
- .getAlignment().getSequences());
+ originalSource.firePropertyChange("alignment", null,
+ originalSource.getAlignment().getSequences());
}
/**
// != null;
updateEditMenuBar();
- originalSource.firePropertyChange("alignment", null, originalSource
- .getAlignment().getSequences());
+ originalSource.firePropertyChange("alignment", null,
+ originalSource.getAlignment().getSequences());
}
AlignmentViewport getOriginatingSource(CommandI command)
{
EditCommand editCommand = (EditCommand) command;
al = editCommand.getAlignment();
- Vector comps = (Vector) PaintRefresher.components.get(viewport
- .getSequenceSetId());
+ Vector comps = (Vector) PaintRefresher.components
+ .get(viewport.getSequenceSetId());
for (int i = 0; i < comps.size(); i++)
{
if (comps.elementAt(i) instanceof AlignmentPanel)
List<SequenceI> sg = new Vector<>();
if (viewport.cursorMode)
{
- sg.add(viewport.getAlignment().getSequenceAt(
- alignPanel.seqPanel.seqCanvas.cursorY));
+ sg.add(viewport.getAlignment()
+ .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
}
else if (viewport.getSelectionGroup() != null
&& viewport.getSelectionGroup().getSize() != viewport
.getAlignment().getHeight())
{
- sg = viewport.getSelectionGroup().getSequences(
- viewport.getHiddenRepSequences());
+ sg = viewport.getSelectionGroup()
+ .getSequences(viewport.getHiddenRepSequences());
}
if (sg.size() < 1)
SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
- SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
- .size()]);
+ SequenceI[] seqs2 = invertGroup
+ .toArray(new SequenceI[invertGroup.size()]);
for (int i = 0; i < invertGroup.size(); i++)
{
seqs2[i] = invertGroup.elementAt(i);
SlideSequencesCommand ssc;
if (right)
{
- ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
- size, viewport.getGapCharacter());
+ ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
+ viewport.getGapCharacter());
}
else
{
- ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
- size, viewport.getGapCharacter());
+ ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
+ viewport.getGapCharacter());
}
int groupAdjustment = 0;
if (historyList != null && historyList.size() > 0
&& historyList.peek() instanceof SlideSequencesCommand)
{
- appendHistoryItem = ssc
- .appendSlideCommand((SlideSequencesCommand) historyList
- .peek());
+ appendHistoryItem = ssc.appendSlideCommand(
+ (SlideSequencesCommand) historyList.peek());
}
if (!appendHistoryItem)
endRes += seq.getStart() - 1;
}
- copiedSequences.append(seq.getName()
- + "\t"
- + startRes
- + "\t"
- + endRes
- + "\t"
- + seq.getSequenceAsString(sg.getStartRes(),
- sg.getEndRes() + 1) + "\n");
+ copiedSequences.append(seq.getName() + "\t" + startRes + "\t" + endRes
+ + "\t" + seq.getSequenceAsString(sg.getStartRes(),
+ sg.getEndRes() + 1)
+ + "\n");
}
}
}
else
{
- newtitle = newtitle.concat(MessageManager.formatMessage(
- "label.from_msname", new String[] { getTitle() }));
+ newtitle = newtitle.concat(MessageManager
+ .formatMessage("label.from_msname", new String[]
+ { getTitle() }));
}
AlignFrame af = new AlignFrame(new Alignment(newSeqs),
viewport.applet, newtitle, false);
viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
viewport.getAlignment().getWidth();
- viewport.firePropertyChange("alignment", null, viewport.getAlignment()
- .getSequences());
+ viewport.firePropertyChange("alignment", null,
+ viewport.getAlignment().getSequences());
}
*/
if (sg.getSize() == viewport.getAlignment().getHeight())
{
- boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
- .getAlignment().getWidth()) ? true : false;
+ boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
+ + 1) == viewport.getAlignment().getWidth()) ? true : false;
if (isEntireAlignWidth)
{
String title = MessageManager.getString("label.delete_all");
Panel infoPanel = new Panel();
infoPanel.setLayout(new FlowLayout());
- infoPanel
- .add(new Label(MessageManager.getString("warn.delete_all")));
+ infoPanel.add(
+ new Label(MessageManager.getString("warn.delete_all")));
final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
dialog.setMainPanel(infoPanel);
viewport.setSelectionGroup(null);
viewport.getAlignment().deleteGroup(sg);
- viewport.firePropertyChange("alignment", null, viewport.getAlignment()
- .getSequences());
+ viewport.firePropertyChange("alignment", null,
+ viewport.getAlignment().getSequences());
if (viewport.getAlignment().getHeight() < 1)
{
SequenceI[] seqs;
if (viewport.getSelectionGroup() != null)
{
- seqs = viewport.getSelectionGroup().getSequencesAsArray(
- viewport.getHiddenRepSequences());
+ seqs = viewport.getSelectionGroup()
+ .getSequencesAsArray(viewport.getHiddenRepSequences());
}
else
{
column, al);
}
- statusBar.setText(MessageManager.formatMessage(
- "label.removed_columns",
- new String[] { Integer.valueOf(trimRegion.getSize())
- .toString() }));
+ statusBar.setText(MessageManager
+ .formatMessage("label.removed_columns", new String[]
+ { Integer.valueOf(trimRegion.getSize()).toString() }));
addHistoryItem(trimRegion);
for (SequenceGroup sg : al.getGroups())
SequenceI[] seqs;
if (viewport.getSelectionGroup() != null)
{
- seqs = viewport.getSelectionGroup().getSequencesAsArray(
- viewport.getHiddenRepSequences());
+ seqs = viewport.getSelectionGroup()
+ .getSequencesAsArray(viewport.getHiddenRepSequences());
start = viewport.getSelectionGroup().getStartRes();
end = viewport.getSelectionGroup().getEndRes();
}
addHistoryItem(removeGapCols);
- statusBar.setText(MessageManager.formatMessage(
- "label.removed_empty_columns",
- new String[] { Integer.valueOf(removeGapCols.getSize())
- .toString() }));
+ statusBar.setText(MessageManager
+ .formatMessage("label.removed_empty_columns", new String[]
+ { Integer.valueOf(removeGapCols.getSize()).toString() }));
// This is to maintain viewport position on first residue
// of first sequence
SequenceI[] seqs;
if (viewport.getSelectionGroup() != null)
{
- seqs = viewport.getSelectionGroup().getSequencesAsArray(
- viewport.getHiddenRepSequences());
+ seqs = viewport.getSelectionGroup()
+ .getSequencesAsArray(viewport.getHiddenRepSequences());
start = viewport.getSelectionGroup().getStartRes();
end = viewport.getSelectionGroup().getEndRes();
}
SequenceI seq = al.getSequenceAt(0);
int startRes = seq.findPosition(ranges.getStartRes());
- addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
- al));
+ addHistoryItem(
+ new RemoveGapsCommand("Remove Gaps", seqs, start, end, al));
ranges.setStartRes(seq.findIndex(startRes) - 1);
if (viewport.getAlignment().getAlignmentAnnotation() != null)
{
- for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
+ for (int i = 0; i < viewport.getAlignment()
+ .getAlignmentAnnotation().length; i++)
{
- if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
+ if (!viewport.getAlignment()
+ .getAlignmentAnnotation()[i].autoCalculated)
{
- newal.addAnnotation(viewport.getAlignment()
- .getAlignmentAnnotation()[i]);
+ newal.addAnnotation(
+ viewport.getAlignment().getAlignmentAnnotation()[i]);
}
}
}
PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
newaf.alignPanel.av.getSequenceSetId());
- Vector comps = (Vector) PaintRefresher.components.get(viewport
- .getSequenceSetId());
+ Vector comps = (Vector) PaintRefresher.components
+ .get(viewport.getSequenceSetId());
int viewSize = -1;
for (int i = 0; i < comps.size(); i++)
{
final OverviewPanel overview = new OverviewPanel(alignPanel);
frame.add(overview);
// +50 must allow for applet frame window
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
- "label.overview_params", new String[] { this.getTitle() }),
- overview.getPreferredSize().width,
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager
+ .formatMessage("label.overview_params", new String[]
+ { this.getTitle() }), overview.getPreferredSize().width,
overview.getPreferredSize().height + 50);
frame.pack();
public void sortPairwiseMenuItem_actionPerformed()
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
- .getAlignment().getSequenceAt(0));
+ AlignmentSorter.sortByPID(viewport.getAlignment(),
+ viewport.getAlignment().getSequenceAt(0));
addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
viewport.getAlignment()));
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByID(viewport.getAlignment());
- addHistoryItem(new OrderCommand("ID Sort", oldOrder,
- viewport.getAlignment()));
+ addHistoryItem(
+ new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
SequenceI current;
int Width = viewport.getAlignment().getWidth();
- for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
+ for (int i = 0; i < viewport.getAlignment().getSequences()
+ .size(); i++)
{
current = viewport.getAlignment().getSequenceAt(i);
}
if ((viewport.getSelectionGroup() != null
- && viewport.getSelectionGroup().getSize() < 4 && viewport
- .getSelectionGroup().getSize() > 0)
+ && viewport.getSelectionGroup().getSize() < 4
+ && viewport.getSelectionGroup().getSize() > 0)
|| viewport.getAlignment().getHeight() < 4)
{
return;
protected void njTreeBlosumMenuItem_actionPerformed()
{
- newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, ScoreModels.getInstance()
- .getBlosum62().getName(),
+ newTreePanel(TreeBuilder.NEIGHBOUR_JOINING,
+ ScoreModels.getInstance().getBlosum62().getName(),
"Neighbour joining tree using BLOSUM62");
}
protected void avTreeBlosumMenuItem_actionPerformed()
{
- newTreePanel(TreeBuilder.AVERAGE_DISTANCE, ScoreModels.getInstance()
- .getBlosum62().getName(),
+ newTreePanel(TreeBuilder.AVERAGE_DISTANCE,
+ ScoreModels.getInstance().getBlosum62().getName(),
"Average distance tree using BLOSUM62");
}
SequenceI current;
int Width = viewport.getAlignment().getWidth();
- for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
+ for (int i = 0; i < viewport.getAlignment().getSequences()
+ .size(); i++)
{
current = viewport.getAlignment().getSequenceAt(i);
}
- if ((viewport.getSelectionGroup() != null && viewport
- .getSelectionGroup().getSize() > 1)
+ if ((viewport.getSelectionGroup() != null
+ && viewport.getSelectionGroup().getSize() > 1)
|| (viewport.getAlignment().getHeight() > 1))
{
final TreePanel tp = new TreePanel(alignPanel, type, pwType);
public void sortByTree(TreePanel treePanel, String title)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter
- .sortByTree(viewport.getAlignment(), treePanel.getTree());
+ AlignmentSorter.sortByTree(viewport.getAlignment(),
+ treePanel.getTree());
// addHistoryItem(new HistoryItem("Sort", viewport.alignment,
// HistoryItem.SORT));
- addHistoryItem(new OrderCommand(MessageManager.formatMessage(
- "label.order_by_params", new String[] { title }), oldOrder,
- viewport.getAlignment()));
+ addHistoryItem(new OrderCommand(MessageManager
+ .formatMessage("label.order_by_params", new String[]
+ { title }), oldOrder, viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
// TODO: update this text for each release or centrally store it for
// lite and application
g.setFont(new Font("Helvetica", Font.BOLD, 14));
- g.drawString(MessageManager.formatMessage(
- "label.jalviewLite_release", new String[] { version }), x,
- y += fh);
+ g.drawString(MessageManager
+ .formatMessage("label.jalviewLite_release", new String[]
+ { version }), x, y += fh);
g.setFont(new Font("Helvetica", Font.BOLD, 12));
- g.drawString(MessageManager.formatMessage(
- "label.jaview_build_date", new String[] { builddate }), x,
- y += fh);
+ g.drawString(MessageManager.formatMessage("label.jaview_build_date",
+ new String[]
+ { builddate }), x, y += fh);
g.setFont(new Font("Helvetica", Font.PLAIN, 12));
- g.drawString(MessageManager.getString("label.jalview_authors_1"),
- x, y += fh * 1.5);
+ g.drawString(MessageManager.getString("label.jalview_authors_1"), x,
+ y += fh * 1.5);
g.drawString(MessageManager.getString("label.jalview_authors_2"),
x + 50, y += fh + 8);
- g.drawString(
- MessageManager.getString("label.jalview_dev_managers"), x,
- y += fh);
+ g.drawString(MessageManager.getString("label.jalview_dev_managers"),
+ x, y += fh);
g.drawString(MessageManager
.getString("label.jalview_distribution_lists"), x, y += fh);
g.drawString(MessageManager.getString("label.jalview_please_cite"),
x, y += fh + 8);
g.drawString(
- MessageManager.getString("label.jalview_cite_1_authors"),
- x, y += fh);
- g.drawString(
- MessageManager.getString("label.jalview_cite_1_title"), x,
+ MessageManager.getString("label.jalview_cite_1_authors"), x,
y += fh);
+ g.drawString(MessageManager.getString("label.jalview_cite_1_title"),
+ x, y += fh);
g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
x, y += fh);
}
}
Frame frame = new Frame();
- frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
- .getBuildDate()));
+ frame.add(new AboutPanel(JalviewLite.getVersion(),
+ JalviewLite.getBuildDate()));
jalview.bin.JalviewLite.addFrame(frame,
MessageManager.getString("label.jalview"), 580, 220);
pasteNew.addActionListener(this);
pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
pasteThis.addActionListener(this);
- remove2LeftMenuItem.setLabel(MessageManager
- .getString("action.remove_left"));
+ remove2LeftMenuItem
+ .setLabel(MessageManager.getString("action.remove_left"));
remove2LeftMenuItem.addActionListener(this);
- remove2RightMenuItem.setLabel(MessageManager
- .getString("action.remove_right"));
+ remove2RightMenuItem
+ .setLabel(MessageManager.getString("action.remove_right"));
remove2RightMenuItem.addActionListener(this);
- removeGappedColumnMenuItem.setLabel(MessageManager
- .getString("action.remove_empty_columns"));
+ removeGappedColumnMenuItem.setLabel(
+ MessageManager.getString("action.remove_empty_columns"));
removeGappedColumnMenuItem.addActionListener(this);
- removeAllGapsMenuItem.setLabel(MessageManager
- .getString("action.remove_all_gaps"));
+ removeAllGapsMenuItem
+ .setLabel(MessageManager.getString("action.remove_all_gaps"));
removeAllGapsMenuItem.addActionListener(this);
- removeRedundancyMenuItem.setLabel(MessageManager
- .getString("action.remove_redundancy"));
+ removeRedundancyMenuItem
+ .setLabel(MessageManager.getString("action.remove_redundancy"));
removeRedundancyMenuItem.addActionListener(this);
/*
findMenuItem.addActionListener(this);
selectAllSequenceMenuItem.addActionListener(this);
deselectAllSequenceMenuItem.addActionListener(this);
- invertSequenceMenuItem.setLabel(MessageManager
- .getString("action.invert_sequence_selection"));
+ invertSequenceMenuItem.setLabel(
+ MessageManager.getString("action.invert_sequence_selection"));
invertSequenceMenuItem.addActionListener(this);
- invertColSel.setLabel(MessageManager
- .getString("action.invert_column_selection"));
+ invertColSel.setLabel(
+ MessageManager.getString("action.invert_column_selection"));
invertColSel.addActionListener(this);
- deleteGroups.setLabel(MessageManager
- .getString("action.undefine_groups"));
+ deleteGroups
+ .setLabel(MessageManager.getString("action.undefine_groups"));
deleteGroups.addActionListener(this);
- grpsFromSelection.setLabel(MessageManager
- .getString("action.make_groups_selection"));
+ grpsFromSelection.setLabel(
+ MessageManager.getString("action.make_groups_selection"));
grpsFromSelection.addActionListener(this);
createGroup.setLabel(MessageManager.getString("action.create_group"));
createGroup.addActionListener(this);
unGroup.setLabel(MessageManager.getString("action.remove_group"));
unGroup.addActionListener(this);
- annotationColumnSelection.setLabel(MessageManager
- .getString("action.select_by_annotation"));
+ annotationColumnSelection.setLabel(
+ MessageManager.getString("action.select_by_annotation"));
annotationColumnSelection.addActionListener(this);
/*
Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
hideColumns
.setLabel(MessageManager.getString("label.selected_columns"));
- hideSequences.setLabel(MessageManager
- .getString("label.selected_sequences"));
- hideAllButSelection.setLabel(MessageManager
- .getString("label.all_but_selected_region"));
- hideAllSelection.setLabel(MessageManager
- .getString("label.selected_region"));
- showAllHidden.setLabel(MessageManager
- .getString("label.all_sequences_columns"));
+ hideSequences
+ .setLabel(MessageManager.getString("label.selected_sequences"));
+ hideAllButSelection.setLabel(
+ MessageManager.getString("label.all_but_selected_region"));
+ hideAllSelection
+ .setLabel(MessageManager.getString("label.selected_region"));
+ showAllHidden.setLabel(
+ MessageManager.getString("label.all_sequences_columns"));
showColumns.addActionListener(this);
showSeqs.addActionListener(this);
hideColumns.addActionListener(this);
hideAllButSelection.addActionListener(this);
hideAllSelection.addActionListener(this);
showAllHidden.addActionListener(this);
- featureSettings.setLabel(MessageManager
- .getString("action.feature_settings"));
+ featureSettings
+ .setLabel(MessageManager.getString("action.feature_settings"));
featureSettings.addActionListener(this);
- sequenceFeatures.setLabel(MessageManager
- .getString("label.show_sequence_features"));
+ sequenceFeatures.setLabel(
+ MessageManager.getString("label.show_sequence_features"));
sequenceFeatures.addItemListener(this);
sequenceFeatures.setState(false);
- followMouseOverFlag.setLabel(MessageManager
- .getString("label.automatic_scrolling"));
+ followMouseOverFlag.setLabel(
+ MessageManager.getString("label.automatic_scrolling"));
followMouseOverFlag.addItemListener(this);
alProperties.addActionListener(this);
- overviewMenuItem.setLabel(MessageManager
- .getString("label.overview_window"));
+ overviewMenuItem
+ .setLabel(MessageManager.getString("label.overview_window"));
overviewMenuItem.addActionListener(this);
/*
* Configure Annotations menu items and actions
*/
- annotationPanelMenuItem.setLabel(MessageManager
- .getString("label.show_annotations"));
+ annotationPanelMenuItem
+ .setLabel(MessageManager.getString("label.show_annotations"));
annotationPanelMenuItem.addItemListener(this);
- showGroupConsensus.setLabel(MessageManager
- .getString("label.group_consensus"));
- showGroupConservation.setLabel(MessageManager
- .getString("label.group_conservation"));
- showConsensusHistogram.setLabel(MessageManager
- .getString("label.show_consensus_histogram"));
- showSequenceLogo.setLabel(MessageManager
- .getString("label.show_consensus_logo"));
- normSequenceLogo.setLabel(MessageManager
- .getString("label.norm_consensus_logo"));
- applyAutoAnnotationSettings.setLabel(MessageManager
- .getString("label.apply_all_groups"));
+ showGroupConsensus
+ .setLabel(MessageManager.getString("label.group_consensus"));
+ showGroupConservation
+ .setLabel(MessageManager.getString("label.group_conservation"));
+ showConsensusHistogram.setLabel(
+ MessageManager.getString("label.show_consensus_histogram"));
+ showSequenceLogo.setLabel(
+ MessageManager.getString("label.show_consensus_logo"));
+ normSequenceLogo.setLabel(
+ MessageManager.getString("label.norm_consensus_logo"));
+ applyAutoAnnotationSettings
+ .setLabel(MessageManager.getString("label.apply_all_groups"));
applyAutoAnnotationSettings.setState(true);
Menu autoAnnMenu = new Menu(
MessageManager.getString("label.autocalculated_annotation"));
viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
viewTextMenuItem.setState(true);
viewTextMenuItem.addItemListener(this);
- colourTextMenuItem.setLabel(MessageManager
- .getString("label.colour_text"));
+ colourTextMenuItem
+ .setLabel(MessageManager.getString("label.colour_text"));
colourTextMenuItem.addItemListener(this);
- displayNonconservedMenuItem.setLabel(MessageManager
- .getString("label.show_non_conserved"));
+ displayNonconservedMenuItem
+ .setLabel(MessageManager.getString("label.show_non_conserved"));
displayNonconservedMenuItem.addItemListener(this);
wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
wrapMenuItem.addItemListener(this);
- renderGapsMenuItem.setLabel(MessageManager
- .getString("action.show_gaps"));
+ renderGapsMenuItem
+ .setLabel(MessageManager.getString("action.show_gaps"));
renderGapsMenuItem.setState(true);
renderGapsMenuItem.addItemListener(this);
- centreColumnLabelFlag.setLabel(MessageManager
- .getString("label.centre_column_labels"));
+ centreColumnLabelFlag.setLabel(
+ MessageManager.getString("label.centre_column_labels"));
centreColumnLabelFlag.addItemListener(this);
seqLimits.setState(true);
- seqLimits.setLabel(MessageManager
- .getString("label.show_sequence_limits"));
+ seqLimits.setLabel(
+ MessageManager.getString("label.show_sequence_limits"));
seqLimits.addItemListener(this);
/*
* Configure Colour menu items and actions
*/
- applyToAllGroups.setLabel(MessageManager
- .getString("label.apply_colour_to_all_groups"));
+ applyToAllGroups.setLabel(
+ MessageManager.getString("label.apply_colour_to_all_groups"));
applyToAllGroups.setState(true);
applyToAllGroups.addItemListener(this);
- clustalColour.setLabel(MessageManager
- .getString("label.colourScheme_clustal"));
+ clustalColour.setLabel(
+ MessageManager.getString("label.colourScheme_clustal"));
clustalColour.addActionListener(this);
- zappoColour.setLabel(MessageManager
- .getString("label.colourScheme_zappo"));
+ zappoColour
+ .setLabel(MessageManager.getString("label.colourScheme_zappo"));
zappoColour.addActionListener(this);
- taylorColour.setLabel(MessageManager
- .getString("label.colourScheme_taylor"));
+ taylorColour.setLabel(
+ MessageManager.getString("label.colourScheme_taylor"));
taylorColour.addActionListener(this);
- hydrophobicityColour.setLabel(MessageManager
- .getString("label.colourScheme_hydrophobic"));
+ hydrophobicityColour.setLabel(
+ MessageManager.getString("label.colourScheme_hydrophobic"));
hydrophobicityColour.addActionListener(this);
helixColour.setLabel(MessageManager
.getString("label.colourScheme_helix_propensity"));
strandColour.setLabel(MessageManager
.getString("label.colourScheme_strand_propensity"));
strandColour.addActionListener(this);
- turnColour.setLabel(MessageManager
- .getString("label.colourScheme_turn_propensity"));
+ turnColour.setLabel(
+ MessageManager.getString("label.colourScheme_turn_propensity"));
turnColour.addActionListener(this);
- buriedColour.setLabel(MessageManager
- .getString("label.colourScheme_buried_index"));
+ buriedColour.setLabel(
+ MessageManager.getString("label.colourScheme_buried_index"));
buriedColour.addActionListener(this);
purinePyrimidineColour.setLabel(MessageManager
.getString("label.colourScheme_purine/pyrimidine"));
// RNAInteractionColour.setLabel(MessageManager
// .getString("label.rna_interaction"));
// RNAInteractionColour.addActionListener(this);
- RNAHelixColour.setLabel(MessageManager
- .getString("label.colourScheme_rna_helices"));
+ RNAHelixColour.setLabel(
+ MessageManager.getString("label.colourScheme_rna_helices"));
RNAHelixColour.addActionListener(this);
- userDefinedColour.setLabel(MessageManager
- .getString("action.user_defined"));
+ userDefinedColour
+ .setLabel(MessageManager.getString("action.user_defined"));
userDefinedColour.addActionListener(this);
- PIDColour.setLabel(MessageManager
- .getString("label.colourScheme_%_identity"));
+ PIDColour.setLabel(
+ MessageManager.getString("label.colourScheme_%_identity"));
PIDColour.addActionListener(this);
- BLOSUM62Colour.setLabel(MessageManager
- .getString("label.colourScheme_blosum62"));
+ BLOSUM62Colour.setLabel(
+ MessageManager.getString("label.colourScheme_blosum62"));
BLOSUM62Colour.addActionListener(this);
- tcoffeeColour.setLabel(MessageManager
- .getString("label.colourScheme_t-coffee_scores"));
+ tcoffeeColour.setLabel(
+ MessageManager.getString("label.colourScheme_t-coffee_scores"));
// it will be enabled only if a score file is provided
tcoffeeColour.setEnabled(false);
tcoffeeColour.addActionListener(this);
- conservationMenuItem.setLabel(MessageManager
- .getString("action.by_conservation"));
+ conservationMenuItem
+ .setLabel(MessageManager.getString("action.by_conservation"));
conservationMenuItem.addItemListener(this);
noColourmenuItem.setLabel(MessageManager.getString("label.none"));
noColourmenuItem.addActionListener(this);
- abovePIDThreshold.setLabel(MessageManager
- .getString("label.above_identity_threshold"));
+ abovePIDThreshold.setLabel(
+ MessageManager.getString("label.above_identity_threshold"));
abovePIDThreshold.addItemListener(this);
- nucleotideColour.setLabel(MessageManager
- .getString("label.colourScheme_nucleotide"));
+ nucleotideColour.setLabel(
+ MessageManager.getString("label.colourScheme_nucleotide"));
nucleotideColour.addActionListener(this);
- modifyPID.setLabel(MessageManager
- .getString("label.modify_identity_threshold"));
+ modifyPID.setLabel(
+ MessageManager.getString("label.modify_identity_threshold"));
modifyPID.setEnabled(abovePIDThreshold.getState());
modifyPID.addActionListener(this);
modifyConservation.setLabel(MessageManager
.getString("label.modify_conservation_threshold"));
modifyConservation.setEnabled(conservationMenuItem.getState());
modifyConservation.addActionListener(this);
- annotationColour.setLabel(MessageManager
- .getString("action.by_annotation"));
+ annotationColour
+ .setLabel(MessageManager.getString("action.by_annotation"));
annotationColour.addActionListener(this);
/*
* Configure Calculate menu items and actions
*/
- sortPairwiseMenuItem.setLabel(MessageManager
- .getString("action.by_pairwise_id"));
+ sortPairwiseMenuItem
+ .setLabel(MessageManager.getString("action.by_pairwise_id"));
sortPairwiseMenuItem.addActionListener(this);
sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
sortIDMenuItem.addActionListener(this);
- sortLengthMenuItem.setLabel(MessageManager
- .getString("action.by_length"));
+ sortLengthMenuItem
+ .setLabel(MessageManager.getString("action.by_length"));
sortLengthMenuItem.addActionListener(this);
sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
sortGroupMenuItem.addActionListener(this);
- pairwiseAlignmentMenuItem.setLabel(MessageManager
- .getString("action.pairwise_alignment"));
+ pairwiseAlignmentMenuItem.setLabel(
+ MessageManager.getString("action.pairwise_alignment"));
pairwiseAlignmentMenuItem.addActionListener(this);
- PCAMenuItem.setLabel(MessageManager
- .getString("label.principal_component_analysis"));
+ PCAMenuItem.setLabel(
+ MessageManager.getString("label.principal_component_analysis"));
PCAMenuItem.addActionListener(this);
autoCalculate = new CheckboxMenuItem(
- MessageManager.getString("label.autocalculate_consensus"), true);
- averageDistanceTreeMenuItem.setLabel(MessageManager
- .getString("label.average_distance_identity"));
+ MessageManager.getString("label.autocalculate_consensus"),
+ true);
+ averageDistanceTreeMenuItem.setLabel(
+ MessageManager.getString("label.average_distance_identity"));
averageDistanceTreeMenuItem.addActionListener(this);
- neighbourTreeMenuItem.setLabel(MessageManager
- .getString("label.neighbour_joining_identity"));
+ neighbourTreeMenuItem.setLabel(
+ MessageManager.getString("label.neighbour_joining_identity"));
neighbourTreeMenuItem.addActionListener(this);
- avDistanceTreeBlosumMenuItem.setLabel(MessageManager
- .getString("label.average_distance_blosum62"));
+ avDistanceTreeBlosumMenuItem.setLabel(
+ MessageManager.getString("label.average_distance_blosum62"));
avDistanceTreeBlosumMenuItem.addActionListener(this);
- njTreeBlosumMenuItem.setLabel(MessageManager
- .getString("label.neighbour_blosum62"));
+ njTreeBlosumMenuItem
+ .setLabel(MessageManager.getString("label.neighbour_blosum62"));
njTreeBlosumMenuItem.addActionListener(this);
- sortByTreeMenu.setLabel(MessageManager
- .getString("action.by_tree_order"));
+ sortByTreeMenu
+ .setLabel(MessageManager.getString("action.by_tree_order"));
Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
Menu calculateTreeMenu = new Menu(
MessageManager.getString("action.calculate_tree"));
theApplet.add(embeddedMenu, BorderLayout.NORTH);
theApplet.add(statusBar, BorderLayout.SOUTH);
// TODO should size be left to the layout manager?
- alignPanel.setSize(theApplet.getSize().width,
- theApplet.getSize().height - embeddedMenu.getHeight()
- - statusBar.getHeight());
+ alignPanel.setSize(theApplet.getSize().width, theApplet.getSize().height
+ - embeddedMenu.getHeight() - statusBar.getHeight());
theApplet.add(alignPanel, BorderLayout.CENTER);
final AlignFrame me = this;
theApplet.addFocusListener(new FocusListener()
viewer = (Viewer) jmolviewer;
} catch (ClassCastException ex)
{
- System.err.println("Unsupported viewer object :"
- + jmolviewer.getClass());
+ System.err.println(
+ "Unsupported viewer object :" + jmolviewer.getClass());
}
if (viewer == null)
{
}
// resolve data source
// TODO: this code should be a refactored to an io package
- DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
- pdbFile, FileFormat.PDB);
+ DataSourceType protocol = AppletFormatAdapter.resolveProtocol(pdbFile,
+ FileFormat.PDB);
if (protocol == null)
{
return false;
{
if (seqs[i] != null)
{
- sequences.addElement(new Object[] { seqs[i],
- (chains != null) ? chains[i] : null });
+ sequences
+ .addElement(new Object[]
+ { seqs[i], (chains != null) ? chains[i] : null });
}
}
seqs = new SequenceI[sequences.size()];
chains = (String[]) sqch[1];
if (seqs == null || seqs.length == 0)
{
- System.err
- .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
+ System.err.println(
+ "JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
}
if (protocol == null)
{
}
if (ajm != null)
{
- System.err
- .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
+ System.err.println(
+ "Incremental adding and aligning structure to existing Jmol view not yet implemented.");
// try and add the pdb structure
// ajm.addS
ajm = null;
// otherwise, create a new window
if (applet.jmolAvailable)
{
- new AppletJmol(pdb, seqs, chains, alignPanel,
- protocol);
+ new AppletJmol(pdb, seqs, chains, alignPanel, protocol);
applet.lastFrameX += 40;
applet.lastFrameY += 40;
}
*/
AlignmentI aln;
if ((aln = viewport.getAlignment()) != null
- && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
- .getWidth()))
+ && (aln.getHeight() != file.getHeight()
+ || aln.getWidth() != file.getWidth()))
{
// TODO: raise a dialog box here rather than bomb out.
- System.err
- .println("The scores matrix does not match the alignment dimensions");
+ System.err.println(
+ "The scores matrix does not match the alignment dimensions");
}
import java.awt.Font;
import java.awt.FontMetrics;
-public class AlignViewport extends AlignmentViewport implements
- SelectionSource
+public class AlignViewport extends AlignmentViewport
+ implements SelectionSource
{
boolean cursorMode = false;
}
if (widthScale <= 1.0)
{
- System.err
- .println("Invalid alignment character width scaling factor ("
+ System.err.println(
+ "Invalid alignment character width scaling factor ("
+ widthScale + "). Ignoring.");
widthScale = 1;
}
if (JalviewLite.debug)
{
- System.err
- .println("Alignment character width scaling factor is now "
+ System.err.println(
+ "Alignment character width scaling factor is now "
+ widthScale);
}
}
}
if (heightScale <= 1.0)
{
- System.err
- .println("Invalid alignment character height scaling factor ("
+ System.err.println(
+ "Invalid alignment character height scaling factor ("
+ heightScale + "). Ignoring.");
heightScale = 1;
}
if (JalviewLite.debug)
{
- System.err
- .println("Alignment character height scaling factor is now "
+ System.err.println(
+ "Alignment character height scaling factor is now "
+ heightScale);
}
}
if (applet != null)
{
- setShowJVSuffix(applet.getDefaultParameter("showFullId",
- getShowJVSuffix()));
+ setShowJVSuffix(
+ applet.getDefaultParameter("showFullId", getShowJVSuffix()));
setShowAnnotation(applet.getDefaultParameter("showAnnotation",
isShowAnnotation()));
setShowUnconserved(applet.getDefaultParameter("showUnconserved",
getShowUnconserved()));
- setScaleProteinAsCdna(applet.getDefaultParameter(
- "scaleProteinAsCdna", isScaleProteinAsCdna()));
+ setScaleProteinAsCdna(applet.getDefaultParameter("scaleProteinAsCdna",
+ isScaleProteinAsCdna()));
String param = applet.getParameter("upperCase");
if (param != null)
if (applet != null)
{
- String colour = al.isNucleotide() ? applet
- .getParameter("defaultColourNuc") : applet
- .getParameter("defaultColourProt");
+ String colour = al.isNucleotide()
+ ? applet.getParameter("defaultColourNuc")
+ : applet.getParameter("defaultColourProt");
if (colour == null)
{
colour = applet.getParameter("defaultColour");
if (applet.getParameter("userDefinedColour") != null)
{
- residueShading = new ResidueShader(
- new UserColourScheme(
- applet.getParameter("userDefinedColour")));
+ residueShading = new ResidueShader(new UserColourScheme(
+ applet.getParameter("userDefinedColour")));
}
}
initAutoAnnotation();
{
Font f2 = new Font(f.getName(), Font.BOLD, f.getSize());
FontMetrics fm = nullFrame.getGraphics().getFontMetrics(f2);
- setCharWidth((int) (widthScale * (fm.stringWidth("MMMMMMMMMMM") / 10)));
+ setCharWidth(
+ (int) (widthScale * (fm.stringWidth("MMMMMMMMMMM") / 10)));
}
}
import java.beans.PropertyChangeEvent;
import java.util.List;
-public class AlignmentPanel extends Panel implements AdjustmentListener,
- AlignmentViewPanel, ViewportListenerI
+public class AlignmentPanel extends Panel
+ implements AdjustmentListener, AlignmentViewPanel, ViewportListenerI
{
public AlignViewport av;
idPanel.idCanvas.image = null;
FontMetrics fm = getFontMetrics(av.getFont());
- scalePanel.setSize(new Dimension(10, av.getCharHeight()
- + fm.getDescent()));
- idwidthAdjuster.setSize(new Dimension(10, av.getCharHeight()
- + fm.getDescent()));
+ scalePanel.setSize(
+ new Dimension(10, av.getCharHeight() + fm.getDescent()));
+ idwidthAdjuster.setSize(
+ new Dimension(10, av.getCharHeight() + fm.getDescent()));
av.updateSequenceIdColours();
annotationPanel.image = null;
int ap = annotationPanel.adjustPanelHeight(false);
* @return false if results were not found
*/
public boolean scrollToPosition(SearchResultsI results,
- int verticalOffset,
- boolean redrawOverview, boolean centre)
+ int verticalOffset, boolean redrawOverview, boolean centre)
{
// do we need to scroll the panel?
if (results != null && results.getSize() > 0)
{
if (JalviewLite.debug)
{// DEBUG
- System.out
- .println("DEBUG: scroll didn't happen - results not within alignment : "
+ System.out.println(
+ "DEBUG: scroll didn't happen - results not within alignment : "
+ seq.getStart() + "," + seq.getEnd());
}
return false;
*/
if (centre)
{
- int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2 - 1;
+ int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2
+ - 1;
start = Math.max(start - offset, 0);
end = end + offset - 1;
// end = Math.min(end + offset, seq.getEnd() - 1);
/*
* Scroll down to make end of search results visible
*/
- setScrollValues(vpRanges.getStartRes(), starts + seqIndex - ends
- + 1);
+ setScrollValues(vpRanges.getStartRes(),
+ starts + seqIndex - ends + 1);
}
/*
* Else results are already visible - no need to scroll
// this is called after loading new annotation onto alignment
if (alignFrame.getSize().height == 0)
{
- System.out
- .println("adjustAnnotationHeight frame size zero NEEDS FIXING");
+ System.out.println(
+ "adjustAnnotationHeight frame size zero NEEDS FIXING");
}
fontChanged();
validateAnnotationDimensions(true);
*/
if (annotationHeight + alignmentHeight > availableHeight)
{
- annotationHeight = Math.min(annotationHeight, availableHeight - 2
- * rowHeight);
+ annotationHeight = Math.min(annotationHeight,
+ availableHeight - 2 * rowHeight);
}
}
else
annotationPanel.setSize(new Dimension(d.width, annotationHeight));
annotationPanelHolder.setSize(new Dimension(d.width, annotationHeight));
// seqPanelHolder.setSize(d.width, seqandannot - height);
- seqPanel.seqCanvas
- .setSize(d.width, seqPanel.seqCanvas.getSize().height);
+ seqPanel.seqCanvas.setSize(d.width,
+ seqPanel.seqCanvas.getSize().height);
Dimension e = idPanel.getSize();
alabels.setSize(new Dimension(e.width, annotationHeight));
- annotationSpaceFillerHolder.setSize(new Dimension(e.width,
- annotationHeight));
+ annotationSpaceFillerHolder
+ .setSize(new Dimension(e.width, annotationHeight));
int s = apvscroll.getValue();
if (s > mheight - annotationHeight)
@Override
/**
- * Property change event fired when a change is made to the viewport ranges
+ * Property change event fired when a change is made to the viewport ranges
* object associated with this alignment panel's viewport
*/
public void propertyChange(PropertyChangeEvent evt)
if (oldcs instanceof AnnotationColourGradient)
{
AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
- currentColours.setState(acg.isPredefinedColours()
- || acg.getBaseColour() != null);
+ currentColours.setState(
+ acg.isPredefinedColours() || acg.getBaseColour() != null);
if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
{
minColour.setBackground(acg.getMinColour());
threshold.select(1);
break;
default:
- throw new Error(
- MessageManager
- .getString("error.implementation_error_dont_know_threshold_annotationcolourgradient"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_dont_know_threshold_annotationcolourgradient"));
}
thresholdIsMin.setState(acg.isThresholdIsMinMax());
thresholdValue.setText("" + acg.getAnnotationThreshold());
{
minColour.setBackground(av.applet.getDefaultColourParameter(
"ANNOTATIONCOLOUR_MIN", Color.orange));
- maxColour.setBackground(av.applet.getDefaultColourParameter(
- "ANNOTATIONCOLOUR_MAX", Color.red));
+ maxColour.setBackground(av.applet
+ .getDefaultColourParameter("ANNOTATIONCOLOUR_MAX", Color.red));
}
thresholdValue.setEnabled(false);
thresholdValue.setColumns(5);
currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- currentColours.setLabel(MessageManager
- .getString("label.use_original_colours"));
+ currentColours.setLabel(
+ MessageManager.getString("label.use_original_colours"));
currentColours.addItemListener(this);
thresholdIsMin.setBackground(Color.white);
- thresholdIsMin.setLabel(MessageManager
- .getString("label.threshold_minmax"));
+ thresholdIsMin
+ .setLabel(MessageManager.getString("label.threshold_minmax"));
this.setLayout(borderLayout1);
if (!adjusting)
{
thresholdValue.setText((slider.getValue() / 1000f) + "");
- if (currentColours.getState()
- && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
+ if (currentColours.getState() && !(av
+ .getGlobalColourScheme() instanceof AnnotationColourGradient))
{
changeColour();
}
return;
}
- currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annotations
- .getSelectedIndex()];
+ currentAnnotation = av.getAlignment()
+ .getAlignmentAnnotation()[annotations.getSelectedIndex()];
int aboveThreshold = -1;
if (threshold.getSelectedIndex() == 1)
else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
&& currentAnnotation.threshold == null)
{
- currentAnnotation
- .setThreshold(new jalview.datamodel.GraphLine(
- (currentAnnotation.graphMax - currentAnnotation.graphMin) / 2f,
- "Threshold", Color.black));
+ currentAnnotation.setThreshold(new jalview.datamodel.GraphLine(
+ (currentAnnotation.graphMax - currentAnnotation.graphMin)
+ / 2f,
+ "Threshold", Color.black));
}
if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
if (currentColours.getState())
{
- sg.setColourScheme(new AnnotationColourGradient(
- currentAnnotation, sg.getColourScheme(), aboveThreshold));
+ sg.setColourScheme(new AnnotationColourGradient(currentAnnotation,
+ sg.getColourScheme(), aboveThreshold));
}
else
{
- sg.setColourScheme(new AnnotationColourGradient(
- currentAnnotation, minColour.getBackground(), maxColour
- .getBackground(), aboveThreshold));
+ sg.setColourScheme(new AnnotationColourGradient(currentAnnotation,
+ minColour.getBackground(), maxColour.getBackground(),
+ aboveThreshold));
}
}
}
// restore Object state from the previous session if one exists
if (lastChooser != null)
{
- currentSearchPanel = lastChooser
- .getCurrentSearchPanel();
+ currentSearchPanel = lastChooser.getCurrentSearchPanel();
currentStructureFilterPanel = lastChooser
.getCurrentStructureFilterPanel();
- annotations.select(lastChooser
- .getAnnotations().getSelectedIndex());
- threshold.select(lastChooser
- .getThreshold().getSelectedIndex());
- actionOption = lastChooser
- .getActionOption();
+ annotations.select(lastChooser.getAnnotations().getSelectedIndex());
+ threshold.select(lastChooser.getThreshold().getSelectedIndex());
+ actionOption = lastChooser.getActionOption();
percentThreshold.setState(lastChooser.percentThreshold.getState());
}
if (av.getAnnotationColumnSelectionState() != null)
{
- HiddenColumns oldHidden = av
- .getAnnotationColumnSelectionState()
+ HiddenColumns oldHidden = av.getAnnotationColumnSelectionState()
.getOldHiddenColumns();
if (oldHidden != null)
{
}
AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
- setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[getAnnotations()
- .getSelectedIndex()]);
+ setCurrentAnnotation(av.getAlignment()
+ .getAlignmentAnnotation()[getAnnotations().getSelectedIndex()]);
- int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
- .getSelectedIndex());
+ int selectedThresholdItem = getSelectedThresholdItem(
+ getThreshold().getSelectedIndex());
slider.setEnabled(true);
thresholdValue.setEnabled(true);
{
if (getCurrentAnnotation().threshold == null)
{
- getCurrentAnnotation()
- .setThreshold(
- new jalview.datamodel.GraphLine(
- (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
- "Threshold", Color.black));
+ getCurrentAnnotation().setThreshold(new jalview.datamodel.GraphLine(
+ (getCurrentAnnotation().graphMax
+ - getCurrentAnnotation().graphMin) / 2f,
+ "Threshold", Color.black));
}
adjusting = true;
slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
- slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
+ slider.setValue(
+ (int) (getCurrentAnnotation().threshold.value * 1000));
setThresholdValueText();
// slider.setMajorTickSpacing((int) (range / 10f));
slider.setEnabled(true);
adjusting = false;
// build filter params
- filterParams
- .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
+ filterParams.setThresholdType(
+ AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
if (getCurrentAnnotation().isQuantitative())
{
filterParams
if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
{
- filterParams
- .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
+ filterParams.setThresholdType(
+ AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
}
else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
{
- filterParams
- .setThresholdType(AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
+ filterParams.setThresholdType(
+ AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
}
}
}
filterParams.setRegexString(currentSearchPanel.searchBox.getText());
if (currentSearchPanel.displayName.getState())
{
- filterParams
- .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
+ filterParams.addRegexSearchField(
+ AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
}
if (currentSearchPanel.description.getState())
{
- filterParams
- .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
+ filterParams.addRegexSearchField(
+ AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
}
}
else
public void syncState()
{
- if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
+ if (aColChooser
+ .getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
{
furtherAction.select("Hide");
}
}
}
- public class StructureFilterPanel extends TitledPanel implements
- ItemListener
+ public class StructureFilterPanel extends TitledPanel
+ implements ItemListener
{
private AnnotationColumnChooser aColChooser;
import java.util.Collections;
import java.util.Vector;
-public class AnnotationLabels extends Panel implements ActionListener,
- MouseListener, MouseMotionListener
+public class AnnotationLabels extends Panel
+ implements ActionListener, MouseListener, MouseMotionListener
{
Image image;
ap.alignFrame);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, ap.alignFrame.getTitle()
- + " - " + aa[selectedRow].label, 500, 100);
+ jalview.bin.JalviewLite.addFrame(frame,
+ ap.alignFrame.getTitle() + " - " + aa[selectedRow].label, 500,
+ 100);
cap.setText(aa[selectedRow].toString());
}
else if (evt.getActionCommand().equals(COPYCONS_SEQ))
boolean editLabelDescription(AlignmentAnnotation annotation)
{
- Checkbox padGaps = new Checkbox("Fill Empty Gaps With \""
- + ap.av.getGapCharacter() + "\"", annotation.padGaps);
+ Checkbox padGaps = new Checkbox(
+ "Fill Empty Gaps With \"" + ap.av.getGapCharacter() + "\"",
+ annotation.padGaps);
EditNameDialog dialog = new EditNameDialog(annotation.label,
annotation.description, " Annotation Label",
if (resizePanel)
{
- Dimension d = ap.annotationPanelHolder.getSize(), e = ap.annotationSpaceFillerHolder
- .getSize(), f = ap.seqPanelHolder.getSize();
+ Dimension d = ap.annotationPanelHolder.getSize(),
+ e = ap.annotationSpaceFillerHolder.getSize(),
+ f = ap.seqPanelHolder.getSize();
int dif = evt.getY() - oldY;
dif /= ap.av.getCharHeight();
{
ap.annotationPanel.setSize(d.width, d.height - dif);
setSize(new Dimension(e.width, d.height - dif));
- ap.annotationSpaceFillerHolder.setSize(new Dimension(e.width,
- d.height - dif));
- ap.annotationPanelHolder.setSize(new Dimension(d.width, d.height
- - dif));
+ ap.annotationSpaceFillerHolder
+ .setSize(new Dimension(e.width, d.height - dif));
+ ap.annotationPanelHolder
+ .setSize(new Dimension(d.width, d.height - dif));
ap.apvscroll.setValues(ap.apvscroll.getValue(), d.height - dif, 0,
av.calcPanelHeight());
f.height += dif;
ap.seqPanelHolder.setPreferredSize(f);
- ap.setScrollValues(av.getRanges().getStartRes(), av.getRanges()
- .getStartSeq());
+ ap.setScrollValues(av.getRanges().getStartRes(),
+ av.getRanges().getStartSeq());
ap.validate();
// ap.paintAlignment(true);
ap.addNotify();
.getAlignmentAnnotation();
// DETECT RIGHT MOUSE BUTTON IN AWT
- if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+ if ((evt.getModifiers()
+ & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
{
PopupMenu popup = new PopupMenu(
popup.addSeparator();
final CheckboxMenuItem cbmi = new CheckboxMenuItem(
MessageManager.getString("label.ignore_gaps_consensus"),
- (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
- .getIgnoreGapsConsensus() : ap.av
- .isIgnoreGapsConsensus());
+ (aa[selectedRow].groupRef != null)
+ ? aa[selectedRow].groupRef
+ .getIgnoreGapsConsensus()
+ : ap.av.isIgnoreGapsConsensus());
final AlignmentAnnotation aaa = aa[selectedRow];
cbmi.addItemListener(new ItemListener()
{
// can be
// updated.
av.setShowConsensusHistogram(chist.getState());
- ap.alignFrame.showConsensusHistogram.setState(chist
- .getState()); // TODO: implement
- // ap.updateGUI()/alignFrame.updateGUI
- // for applet
+ ap.alignFrame.showConsensusHistogram
+ .setState(chist.getState()); // TODO: implement
+ // ap.updateGUI()/alignFrame.updateGUI
+ // for applet
ap.repaint();
// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
}
// can be
// updated.
av.setShowSequenceLogo(true);
- ap.alignFrame.normSequenceLogo.setState(cprofn.getState()); // TODO:
- // implement
- // ap.updateGUI()/alignFrame.updateGUI
- // for
- // applet
+ ap.alignFrame.normSequenceLogo
+ .setState(cprofn.getState()); // TODO:
+ // implement
+ // ap.updateGUI()/alignFrame.updateGUI
+ // for
+ // applet
av.setNormaliseSequenceLogo(cprofn.getState());
ap.repaint();
// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
ap.seqPanel.ap.idPanel.highlightSearchResults(null);
// process modifiers
SequenceGroup sg = ap.av.getSelectionGroup();
- if (sg == null
- || sg == aa[selectedRow].groupRef
- || !(jalview.util.Platform.isControlDown(evt) || evt
- .isShiftDown()))
+ if (sg == null || sg == aa[selectedRow].groupRef
+ || !(jalview.util.Platform.isControlDown(evt)
+ || evt.isShiftDown()))
{
if (jalview.util.Platform.isControlDown(evt)
|| evt.isShiftDown())
{
// clone a new selection group from the associated group
- ap.av.setSelectionGroup(new SequenceGroup(
- aa[selectedRow].groupRef));
+ ap.av.setSelectionGroup(
+ new SequenceGroup(aa[selectedRow].groupRef));
}
else
{
}
else
{
- ap.seqPanel.ap.idPanel
- .highlightSearchResults(aa[selectedRow].groupRef
- .getSequences(null));
+ ap.seqPanel.ap.idPanel.highlightSearchResults(
+ aa[selectedRow].groupRef.getSequences(null));
}
return;
}
if (evt.getClickCount() == 1)
{
ap.seqPanel.ap.idPanel
- .highlightSearchResults(Arrays
- .asList(new SequenceI[] { aa[selectedRow].sequenceRef }));
+ .highlightSearchResults(Arrays.asList(new SequenceI[]
+ { aa[selectedRow].sequenceRef }));
}
else if (evt.getClickCount() >= 2)
{
// we make a copy rather than edit the current selection if no
// modifiers pressed
// see Enhancement JAL-1557
- if (!(jalview.util.Platform.isControlDown(evt) || evt
- .isShiftDown()))
+ if (!(jalview.util.Platform.isControlDown(evt)
+ || evt.isShiftDown()))
{
sg = new SequenceGroup(sg);
sg.clear();
return;
}
jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer();
- jalview.appletgui.AlignFrame.copiedSequences.append(sq.getName() + "\t"
- + sq.getStart() + "\t" + sq.getEnd() + "\t"
- + sq.getSequenceAsString() + "\n");
+ jalview.appletgui.AlignFrame.copiedSequences
+ .append(sq.getName() + "\t" + sq.getStart() + "\t" + sq.getEnd()
+ + "\t" + sq.getSequenceAsString() + "\n");
if (av.hasHiddenColumns())
{
jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector<>(
- av.getAlignment().getHiddenColumns()
- .getHiddenColumnsCopy());
+ av.getAlignment().getHiddenColumns().getHiddenColumnsCopy());
}
}
import java.awt.event.MouseMotionListener;
import java.beans.PropertyChangeEvent;
-public class AnnotationPanel extends Panel implements AwtRenderPanelI,
- AdjustmentListener, ActionListener, MouseListener,
- MouseMotionListener, ViewportListenerI
+public class AnnotationPanel extends Panel
+ implements AwtRenderPanelI, AdjustmentListener, ActionListener,
+ MouseListener, MouseMotionListener, ViewportListenerI
{
AlignViewport av;
if (anot.length < av.getColumnSelection().getMax())
{
- Annotation[] temp = new Annotation[av.getColumnSelection().getMax() + 2];
+ Annotation[] temp = new Annotation[av.getColumnSelection().getMax()
+ + 2];
System.arraycopy(anot, 0, temp, 0, anot.length);
anot = temp;
aa[activeRow].annotations = anot;
anot[index] = new Annotation(label, "", type, 0);
}
- anot[index].secondaryStructure = type != 'S' ? type : label
- .length() == 0 ? ' ' : label.charAt(0);
+ anot[index].secondaryStructure = type != 'S' ? type
+ : label.length() == 0 ? ' ' : label.charAt(0);
anot[index].displayCharacter = label;
}
}
}
}
- if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK
+ if ((evt.getModifiers()
+ & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK
&& activeRow != -1)
{
if (av.getColumnSelection() == null
{
if (graphStretch > -1)
{
- av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY
- - evt.getY();
- if (av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight < 0)
+ av.getAlignment()
+ .getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY
+ - evt.getY();
+ if (av.getAlignment()
+ .getAlignmentAnnotation()[graphStretch].graphHeight < 0)
{
- av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight = 0;
+ av.getAlignment()
+ .getAlignmentAnnotation()[graphStretch].graphHeight = 0;
}
graphStretchY = evt.getY();
av.calcPanelHeight();
String name;
if (av.getAlignment().isNucleotide())
{
- name = ResidueProperties.nucleotideName.get(String
- .valueOf(residue));
- text.append(" Nucleotide: ").append(
- name != null ? name : residue);
+ name = ResidueProperties.nucleotideName
+ .get(String.valueOf(residue));
+ text.append(" Nucleotide: ")
+ .append(name != null ? name : residue);
}
else
{
- name = 'X' == residue ? "X" : ('*' == residue ? "STOP"
- : ResidueProperties.aa2Triplet.get(String
- .valueOf(residue)));
- text.append(" Residue: ").append(
- name != null ? name : residue);
+ name = 'X' == residue ? "X"
+ : ('*' == residue ? "STOP"
+ : ResidueProperties.aa2Triplet
+ .get(String.valueOf(residue)));
+ text.append(" Residue: ")
+ .append(name != null ? name : residue);
}
int residuePos = seqref.findPosition(column);
text.append(" (").append(residuePos).append(")");
gg.setColor(Color.white);
gg.fillRect(0, 0, getSize().width, getSize().height);
- drawComponent(gg, av.getRanges().getStartRes(), av.getRanges()
- .getEndRes() + 1);
+ drawComponent(gg, av.getRanges().getStartRes(),
+ av.getRanges().getEndRes() + 1);
g.drawImage(image, 0, 0, this);
}
gg.copyArea(0, 0, imgWidth, getSize().height,
-horizontal * av.getCharWidth(), 0);
- int sr = av.getRanges().getStartRes(), er = av.getRanges().getEndRes() + 1, transX = 0;
+ int sr = av.getRanges().getStartRes(),
+ er = av.getRanges().getEndRes() + 1, transX = 0;
if (horizontal > 0) // scrollbar pulled right, image to the left
{
thresholdValue.setCaretPosition(0);
adjusting = oldadj;
}
-
+
public void thresholdValue_actionPerformed(ActionEvent e)
{
try
if (percentThreshold.getState())
{
int pos = slider.getMinimum()
- + (int) ((slider.getMaximum() - slider.getMinimum()) * f / 100f);
+ + (int) ((slider.getMaximum() - slider.getMinimum()) * f
+ / 100f);
slider.setValue(pos);
}
else
import java.util.Vector;
public class AppletJmol extends EmbmenuFrame implements
-// StructureListener,
+ // StructureListener,
KeyListener, ActionListener, ItemListener
{
CheckboxMenuItem jmolColour = new CheckboxMenuItem(
MessageManager.getString("action.using_jmol"), false);
- MenuItem chain = new MenuItem(MessageManager.getString("action.by_chain"));
+ MenuItem chain = new MenuItem(
+ MessageManager.getString("action.by_chain"));
MenuItem charge = new MenuItem(
MessageManager.getString("label.charge_cysteine"));
{
this.ap = ap;
jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(),
- new PDBEntry[] { pdbentry }, new SequenceI[][] { seq },
- protocol);
+ new PDBEntry[]
+ { pdbentry }, new SequenceI[][] { seq }, protocol);
jmb.setColourBySequence(true);
if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
{
if (protocol == DataSourceType.PASTE)
{
- pdbentry.setId("PASTED PDB"
- + (chains == null ? "_" : chains.toString()));
+ pdbentry.setId(
+ "PASTED PDB" + (chains == null ? "_" : chains.toString()));
}
else
{
StructureFile reader = null;
if (alreadyMapped != null)
{
- reader = StructureSelectionManager.getStructureSelectionManager(
- ap.av.applet).setMapping(seq, chains, pdbentry.getFile(),
- protocol);
+ reader = StructureSelectionManager
+ .getStructureSelectionManager(ap.av.applet)
+ .setMapping(seq, chains, pdbentry.getFile(), protocol);
// PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW?
// FOR NOW, LETS JUST OPEN A NEW WINDOW
}
try
{
- jmb.allocateViewer(renderPanel, true, ap.av.applet.getName()
- + "_jmol_", ap.av.applet.getDocumentBase(),
- ap.av.applet.getCodeBase(), "-applet", scriptWindow, null);
+ jmb.allocateViewer(renderPanel, true,
+ ap.av.applet.getName() + "_jmol_",
+ ap.av.applet.getDocumentBase(), ap.av.applet.getCodeBase(),
+ "-applet", scriptWindow, null);
} catch (Exception e)
{
- System.err
- .println("Couldn't create a jmol viewer. Args to allocate viewer were:\nDocumentBase="
- + ap.av.applet.getDocumentBase()
- + "\nCodebase="
+ System.err.println(
+ "Couldn't create a jmol viewer. Args to allocate viewer were:\nDocumentBase="
+ + ap.av.applet.getDocumentBase() + "\nCodebase="
+ ap.av.applet.getCodeBase());
e.printStackTrace();
dispose();
});
pdbentry.setProperty("protocol", protocol);
if (pdbentry.getFile() != null)
-
+
{
// import structure data from pdbentry.getFile based on given protocol
if (protocol == DataSourceType.PASTE)
{
if (jalview.bin.JalviewLite.debug)
{
- System.err
- .println("AppletJmol:Trying to reuse existing PDBfile IO parser.");
+ System.err.println(
+ "AppletJmol:Trying to reuse existing PDBfile IO parser.");
}
// re-use the one we opened earlier
freader = reader.getReader();
{
if (jalview.bin.JalviewLite.debug)
{
- System.err
- .println("AppletJmol:Creating new PDBfile IO parser.");
+ System.err.println(
+ "AppletJmol:Creating new PDBfile IO parser.");
}
FileParse fp = new FileParse(pdbentry.getFile(), protocol);
fp.mark();
}
if (freader == null)
{
- throw new Exception(
- MessageManager
- .getString("exception.invalid_datasource_couldnt_obtain_reader"));
+ throw new Exception(MessageManager.getString(
+ "exception.invalid_datasource_couldnt_obtain_reader"));
}
jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(),
freader);
} catch (OutOfMemoryError ex)
{
frame.dispose();
- System.err
- .println("Out of memory when trying to create dialog box with sequence-structure mapping.");
+ System.err.println(
+ "Out of memory when trying to create dialog box with sequence-structure mapping.");
return;
}
jalview.bin.JalviewLite.addFrame(frame,
{
try
{
- ap.av.applet.getAppletContext().showDocument(
- new java.net.URL(
+ ap.av.applet.getAppletContext()
+ .showDocument(new java.net.URL(
"http://jmol.sourceforge.net/docs/JmolUserGuide/"),
- "jmolHelp");
+ "jmolHelp");
} catch (java.net.MalformedURLException ex)
{
}
{
try
{
- appletJmolBinding.ap.av.applet.getAppletContext().showDocument(
- new java.net.URL(url), "jmol");
+ appletJmolBinding.ap.av.applet.getAppletContext()
+ .showDocument(new java.net.URL(url), "jmol");
} catch (java.net.MalformedURLException ex)
{
}
import java.awt.event.MouseListener;
import java.io.IOException;
-public class CutAndPasteTransfer extends Panel implements ActionListener,
- MouseListener
+public class CutAndPasteTransfer extends Panel
+ implements ActionListener, MouseListener
{
boolean pdbImport = false;
// TODO: JAL-1102 - should have a warning message in dialog, not simply
// overwrite the broken input data with the exception
textarea.setText(MessageManager.formatMessage(
- "label.could_not_parse_newick_file",
- new Object[] { ex.getMessage() }));
+ "label.could_not_parse_newick_file", new Object[]
+ { ex.getMessage() }));
return false;
}
return false;
al = afa.readFile(text, DataSourceType.PASTE, format);
source = afa.getAlignFile();
- if (al != null)
- {
- al.setDataset(null); // set dataset on alignment/sequences
-
- /*
- * SplitFrame option dependent on applet parameter for now.
- */
- boolean allowSplitFrame = alignFrame.viewport.applet
- .getDefaultParameter("enableSplitFrame", false);
- if (allowSplitFrame && openSplitFrame(al, format))
+ if (al != null)
{
- return;
- }
- if (newWindow)
- {
- AlignFrame af;
-
- if (source instanceof ComplexAlignFile)
+ al.setDataset(null); // set dataset on alignment/sequences
+
+ /*
+ * SplitFrame option dependent on applet parameter for now.
+ */
+ boolean allowSplitFrame = alignFrame.viewport.applet
+ .getDefaultParameter("enableSplitFrame", false);
+ if (allowSplitFrame && openSplitFrame(al, format))
{
+ return;
+ }
+ if (newWindow)
+ {
+ AlignFrame af;
+
+ if (source instanceof ComplexAlignFile)
+ {
HiddenColumns colSel = ((ComplexAlignFile) source)
.getHiddenColumns();
- SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
- .getHiddenSequences();
- boolean showSeqFeatures = ((ComplexAlignFile) source)
- .isShowSeqFeatures();
- String colourSchemeName = ((ComplexAlignFile) source)
- .getGlobalColourScheme();
- af = new AlignFrame(al, hiddenSeqs, colSel,
- alignFrame.viewport.applet, "Cut & Paste input - "
- + format, false);
- af.getAlignViewport().setShowSequenceFeatures(showSeqFeatures);
- ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
- colourSchemeName, al);
- if (cs != null)
+ SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
+ .getHiddenSequences();
+ boolean showSeqFeatures = ((ComplexAlignFile) source)
+ .isShowSeqFeatures();
+ String colourSchemeName = ((ComplexAlignFile) source)
+ .getGlobalColourScheme();
+ af = new AlignFrame(al, hiddenSeqs, colSel,
+ alignFrame.viewport.applet,
+ "Cut & Paste input - " + format, false);
+ af.getAlignViewport().setShowSequenceFeatures(showSeqFeatures);
+ ColourSchemeI cs = ColourSchemeMapper
+ .getJalviewColourScheme(colourSchemeName, al);
+ if (cs != null)
+ {
+ af.changeColour(cs);
+ }
+ }
+ else
{
- af.changeColour(cs);
+ af = new AlignFrame(al, alignFrame.viewport.applet,
+ "Cut & Paste input - " + format, false);
+ if (source instanceof FeaturesSourceI)
+ {
+ af.getAlignViewport().setShowSequenceFeatures(true);
+ }
}
+
+ af.statusBar.setText(MessageManager.getString(
+ "label.successfully_pasted_annotation_to_alignment"));
}
else
{
- af = new AlignFrame(al, alignFrame.viewport.applet,
- "Cut & Paste input - " + format, false);
- if (source instanceof FeaturesSourceI)
- {
- af.getAlignViewport().setShowSequenceFeatures(true);
- }
+ alignFrame.addSequences(al.getSequencesArray());
+ alignFrame.statusBar.setText(MessageManager
+ .getString("label.successfully_pasted_alignment_file"));
}
-
- af.statusBar
- .setText(MessageManager
- .getString("label.successfully_pasted_annotation_to_alignment"));
}
- else
- {
- alignFrame.addSequences(al.getSequencesArray());
- alignFrame.statusBar.setText(MessageManager
- .getString("label.successfully_pasted_alignment_file"));
- }
- }
} catch (IOException ex)
{
ex.printStackTrace();
alignFrame.alignPanel.fontChanged();
alignFrame.changeColour(new TCoffeeColourScheme(
alignFrame.viewport.getAlignment()));
- alignFrame.statusBar
- .setText(MessageManager
- .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
+ alignFrame.statusBar.setText(MessageManager.getString(
+ "label.successfully_pasted_tcoffee_scores_to_alignment"));
}
else
{
// file valid but didn't get added to alignment for some reason
alignFrame.statusBar.setText(MessageManager.formatMessage(
- "label.failed_add_tcoffee_scores",
- new Object[] { (tcf.getWarningMessage() != null ? tcf
- .getWarningMessage() : "") }));
+ "label.failed_add_tcoffee_scores", new Object[]
+ { (tcf.getWarningMessage() != null
+ ? tcf.getWarningMessage()
+ : "") }));
}
}
else
{
alignFrame.alignPanel.fontChanged();
alignFrame.alignPanel.setScrollValues(0, 0);
- alignFrame.statusBar
- .setText(MessageManager
- .getString("label.successfully_pasted_annotation_to_alignment"));
+ alignFrame.statusBar.setText(MessageManager.getString(
+ "label.successfully_pasted_annotation_to_alignment"));
}
else
if (!alignFrame.parseFeaturesFile(textarea.getText(),
jalview.io.DataSourceType.PASTE))
{
- alignFrame.statusBar
- .setText(MessageManager
- .getString("label.couldnt_parse_pasted_text_as_valid_annotation_feature_GFF_tcoffee_file"));
+ alignFrame.statusBar.setText(MessageManager.getString(
+ "label.couldnt_parse_pasted_text_as_valid_annotation_feature_GFF_tcoffee_file"));
}
}
}
private void jbInit() throws Exception
{
textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 10));
- textarea.setText(MessageManager
- .getString("label.paste_your_alignment_file"));
+ textarea.setText(
+ MessageManager.getString("label.paste_your_alignment_file"));
textarea.addMouseListener(this);
this.setLayout(borderLayout1);
accept.addActionListener(this);
@Override
public void mousePressed(MouseEvent evt)
{
- if (textarea.getText().startsWith(
- MessageManager.getString("label.paste_your")))
+ if (textarea.getText()
+ .startsWith(MessageManager.getString("label.paste_your")))
{
textarea.setText("");
}
if (popup != null)
{
embeddedMenu.add(popup);
- popup.show(embeddedMenu, source.getBounds().x, source.getBounds().y
- + source.getBounds().getSize().height);
+ popup.show(embeddedMenu, source.getBounds().x,
+ source.getBounds().y + source.getBounds().getSize().height);
}
}
private AlignmentPanel ap;
- protected ExtJmol(AlignFrame alframe,
- PDBEntry[] pdbentry, SequenceI[][] seq,
- DataSourceType protocol)
+ protected ExtJmol(AlignFrame alframe, PDBEntry[] pdbentry,
+ SequenceI[][] seq, DataSourceType protocol)
{
super(alframe.alignPanel.getStructureSelectionManager(), pdbentry, seq,
protocol);
{
// This never gets called because we haven't overriden the associated Jmol's
// console
- System.err
- .println("WARNING: unexpected call to ExtJmol's showConsole method. (showConsole="
+ System.err.println(
+ "WARNING: unexpected call to ExtJmol's showConsole method. (showConsole="
+ show);
}
} catch (Exception ex)
{
}
- threshold.select(cs.isAboveThreshold() ? 1 : (cs.isBelowThreshold() ? 2
- : 0));
+ threshold.select(
+ cs.isAboveThreshold() ? 1 : (cs.isBelowThreshold() ? 2 : 0));
adjusting = false;
changeColour(true);
slider.addAdjustmentListener(this);
slider.addMouseListener(this);
owner = (af != null) ? af : fs.frame;
- frame = new JVDialog(owner, MessageManager.formatMessage(
- "label.graduated_color_for_params", new String[] { type }),
- true, 480, 248);
+ frame = new JVDialog(owner, MessageManager
+ .formatMessage("label.graduated_color_for_params", new String[]
+ { type }), true, 480, 248);
frame.setMainPanel(this);
validate();
frame.setVisible(true);
private void jbInit() throws Exception
{
- Label minLabel = new Label(MessageManager.getString("label.min")), maxLabel = new Label(
- MessageManager.getString("label.max"));
+ Label minLabel = new Label(MessageManager.getString("label.min")),
+ maxLabel = new Label(MessageManager.getString("label.max"));
minLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
maxLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
// minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
jPanel3.setBackground(Color.white);
colourFromLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- colourFromLabel.setLabel(MessageManager
- .getString("label.colour_by_label"));
+ colourFromLabel
+ .setLabel(MessageManager.getString("label.colour_by_label"));
colourFromLabel.setSize(new Dimension(139, 22));
// threshold.setBounds(new Rectangle(11, 3, 139, 22));
thresholdIsMin.setBackground(Color.white);
- thresholdIsMin.setLabel(MessageManager
- .getString("label.threshold_minmax"));
+ thresholdIsMin
+ .setLabel(MessageManager.getString("label.threshold_minmax"));
thresholdIsMin.setSize(new Dimension(135, 23));
// thresholdIsMin.setBounds(new Rectangle(328, 3, 135, 23));
jPanel1.add(minLabel);
{
if (newCol == null)
{
- new UserDefinedColours(this,
- minColour.getBackground(), owner,
- MessageManager.getString("label.select_colour_minimum_value"));
+ new UserDefinedColours(this, minColour.getBackground(), owner,
+ MessageManager
+ .getString("label.select_colour_minimum_value"));
}
else
{
{
if (newCol == null)
{
- new UserDefinedColours(this,
- maxColour.getBackground(), owner,
- MessageManager.getString("label.select_colour_maximum_value"));
+ new UserDefinedColours(this, maxColour.getBackground(), owner,
+ MessageManager
+ .getString("label.select_colour_maximum_value"));
}
else
{
adjusting = false;
}
- acg.setAboveThreshold(thresholdOption == AnnotationColourGradient.ABOVE_THRESHOLD);
- acg.setBelowThreshold(thresholdOption == AnnotationColourGradient.BELOW_THRESHOLD);
+ acg.setAboveThreshold(
+ thresholdOption == AnnotationColourGradient.ABOVE_THRESHOLD);
+ acg.setBelowThreshold(
+ thresholdOption == AnnotationColourGradient.BELOW_THRESHOLD);
if (thresholdIsMin.getState()
&& thresholdOption != AnnotationColourGradient.NO_THRESHOLD)
* @author $author$
* @version $Revision$
*/
-public class FeatureRenderer extends
- jalview.renderer.seqfeatures.FeatureRenderer
+public class FeatureRenderer
+ extends jalview.renderer.seqfeatures.FeatureRenderer
{
/*
* creating a new feature defaults to the type and group as
FeatureColourI col = getFeatureStyle(name.getText());
if (col == null)
{
- Color generatedColour = ColorUtils.createColourFromName(name
- .getText());
+ Color generatedColour = ColorUtils
+ .createColourFromName(name.getText());
col = new FeatureColour(generatedColour);
}
tmp = new Panel();
panel.add(tmp);
- tmp.add(new Label(MessageManager.getString("label.name:"), Label.RIGHT));
+ tmp.add(new Label(MessageManager.getString("label.name:"),
+ Label.RIGHT));
tmp.add(name);
tmp = new Panel();
panel.add(tmp);
- tmp.add(new Label(MessageManager.getString("label.group:"), Label.RIGHT));
+ tmp.add(new Label(MessageManager.getString("label.group:"),
+ Label.RIGHT));
tmp.add(group);
tmp = new Panel();
panel.add(tmp);
- tmp.add(new Label(MessageManager.getString("label.colour"), Label.RIGHT));
+ tmp.add(new Label(MessageManager.getString("label.colour"),
+ Label.RIGHT));
tmp.add(colourPanel);
bigPanel.add(panel, BorderLayout.NORTH);
*/
SequenceFeature firstFeature = features.get(0);
boolean useLastDefaults = firstFeature.getType() == null;
- String featureType = useLastDefaults ? lastFeatureAdded : firstFeature
- .getType();
+ String featureType = useLastDefaults ? lastFeatureAdded
+ : firstFeature.getType();
String featureGroup = useLastDefaults ? lastFeatureGroupAdded
: firstFeature.getFeatureGroup();
- String title = create ? MessageManager
- .getString("label.create_new_sequence_features")
+ String title = create
+ ? MessageManager.getString("label.create_new_sequence_features")
: MessageManager.formatMessage("label.amend_delete_features",
- new String[] { sequences.get(0).getName() });
+ new String[]
+ { sequences.get(0).getName() });
final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385,
240);
if (!colourPanel.isGcol)
{
// update colour - otherwise its already done.
- setColour(sf.type, new FeatureColour(colourPanel.getBackground()));
+ setColour(sf.type,
+ new FeatureColour(colourPanel.getBackground()));
}
try
{
{
//
}
- boolean typeOrGroupChanged = (!featureType.equals(sf.type) || !featureGroup
- .equals(sf.featureGroup));
+ boolean typeOrGroupChanged = (!featureType.equals(sf.type)
+ || !featureGroup.equals(sf.featureGroup));
ffile.parseDescriptionHTML(sf, false);
if (typeOrGroupChanged)
{
features.get(i).type = enteredType;
features.get(i).featureGroup = group.getText().trim();
- features.get(i).description = description.getText()
- .replace('\n', ' ');
+ features.get(i).description = description.getText().replace('\n',
+ ' ');
sequences.get(i).addSequenceFeature(features.get(i));
ffile.parseDescriptionHTML(features.get(i), false);
}
import java.util.Set;
import java.util.Vector;
-public class FeatureSettings extends Panel implements ItemListener,
- MouseListener, MouseMotionListener, ActionListener,
- AdjustmentListener, FeatureSettingsControllerI
+public class FeatureSettings extends Panel
+ implements ItemListener, MouseListener, MouseMotionListener,
+ ActionListener, AdjustmentListener, FeatureSettingsControllerI
{
FeatureRenderer fr;
add(lowerPanel, BorderLayout.SOUTH);
- groupPanel.setLayout(new GridLayout(
- (fr.getFeatureGroupsSize()) / 4 + 1, 4)); // JBPNote - this was
- // scaled on number of
- // visible groups. seems
- // broken
+ groupPanel.setLayout(
+ new GridLayout((fr.getFeatureGroupsSize()) / 4 + 1, 4)); // JBPNote
+ // - this
+ // was
+ // scaled
+ // on
+ // number
+ // of
+ // visible
+ // groups.
+ // seems
+ // broken
groupPanel.validate();
add(groupPanel, BorderLayout.NORTH);
public void paint(Graphics g)
{
g.setColor(Color.black);
- g.drawString(MessageManager
- .getString("label.no_features_added_to_this_alignment"), 10, 20);
- g.drawString(MessageManager
- .getString("label.features_can_be_added_from_searches_1"), 10,
- 40);
- g.drawString(MessageManager
- .getString("label.features_can_be_added_from_searches_2"), 10,
- 60);
+ g.drawString(MessageManager.getString(
+ "label.no_features_added_to_this_alignment"), 10, 20);
+ g.drawString(MessageManager.getString(
+ "label.features_can_be_added_from_searches_1"), 10, 40);
+ g.drawString(MessageManager.getString(
+ "label.features_can_be_added_from_searches_2"), 10, 60);
}
protected void popupSort(final MyCheckbox check,
{
final String type = check.type;
final FeatureColourI typeCol = fr.getFeatureStyle(type);
- PopupMenu men = new PopupMenu(MessageManager.formatMessage(
- "label.settings_for_type", new String[] { type }));
+ PopupMenu men = new PopupMenu(MessageManager
+ .formatMessage("label.settings_for_type", new String[]
+ { type }));
java.awt.MenuItem scr = new MenuItem(
MessageManager.getString("label.sort_by_score"));
men.add(scr);
@Override
public void actionPerformed(ActionEvent e)
{
- me.ap.alignFrame.avc.sortAlignmentByFeatureScore(Arrays
- .asList(new String[] { type }));
+ me.ap.alignFrame.avc
+ .sortAlignmentByFeatureScore(Arrays.asList(new String[]
+ { type }));
}
});
@Override
public void actionPerformed(ActionEvent e)
{
- me.ap.alignFrame.avc.sortAlignmentByFeatureDensity(Arrays
- .asList(new String[] { type }));
+ me.ap.alignFrame.avc
+ .sortAlignmentByFeatureDensity(Arrays.asList(new String[]
+ { type }));
}
});
});
men.add(selectContaining);
- MenuItem selectNotContaining = new MenuItem(
- MessageManager.getString("label.select_columns_not_containing"));
+ MenuItem selectNotContaining = new MenuItem(MessageManager
+ .getString("label.select_columns_not_containing"));
selectNotContaining.addActionListener(new ActionListener()
{
@Override
addCheck(groupsChanged, en.nextElement().toString());
}
- featurePanel.setLayout(new GridLayout(featurePanel.getComponentCount(),
- 1, 10, 5));
+ featurePanel.setLayout(
+ new GridLayout(featurePanel.getComponentCount(), 1, 10, 5));
featurePanel.validate();
if (scrollPane != null)
}
else
{
- comp = featurePanel.getComponentAt(evt.getX(), evt.getY()
- + evt.getComponent().getLocation().y);
+ comp = featurePanel.getComponentAt(evt.getX(),
+ evt.getY() + evt.getComponent().getLocation().y);
}
if (comp != null && comp instanceof Checkbox)
for (SearchResultMatchI match : searchResults.getResults())
{
seqs.add(match.getSequence().getDatasetSequence());
- features.add(new SequenceFeature(searchString,
- "Search Results", null, match.getStart(), match.getEnd(),
- "Search Results"));
+ features.add(new SequenceFeature(searchString, "Search Results", null,
+ match.getStart(), match.getEnd(), "Search Results"));
}
if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
// 'SelectRegion' selection
if (!haveResults)
{
- ap.alignFrame.statusBar.setText(MessageManager
- .getString("label.finished_searching"));
+ ap.alignFrame.statusBar.setText(
+ MessageManager.getString("label.finished_searching"));
resIndex = -1;
seqIndex = 0;
}
{
if (findAll)
{
- String message = (idMatch.size() > 0) ? "" + idMatch.size()
- + " IDs" : "";
+ String message = (idMatch.size() > 0) ? "" + idMatch.size() + " IDs"
+ : "";
if (idMatch.size() > 0 && searchResults != null
&& searchResults.getSize() > 0)
{
{
message += searchResults.getSize() + " subsequence matches.";
}
- ap.alignFrame.statusBar.setText(MessageManager.formatMessage(
- "label.search_results", new String[] { searchString,
- message }));
+ ap.alignFrame.statusBar.setText(MessageManager
+ .formatMessage("label.search_results", new String[]
+ { searchString, message }));
}
else
{
// TODO: indicate sequence and matching position in status bar
- ap.alignFrame.statusBar.setText(MessageManager.formatMessage(
- "label.found_match_for", new String[] { searchString }));
+ ap.alignFrame.statusBar.setText(MessageManager
+ .formatMessage("label.found_match_for", new String[]
+ { searchString }));
}
}
}
caseSensitive.setLabel(MessageManager.getString("label.match_case"));
caseSensitive.setBounds(new Rectangle(30, 39, 126, 23));
- searchDescription.setLabel(MessageManager
- .getString("label.include_description"));
+ searchDescription.setLabel(
+ MessageManager.getString("label.include_description"));
searchDescription.setBounds(new Rectangle(30, 59, 170, 23));
actionsPanel.add(findNext, null);
actionsPanel.add(findAll, null);
}
Font newFont = new Font(fontName.getSelectedItem().toString(),
- fontStyle.getSelectedIndex(), Integer.parseInt(fontSize
- .getSelectedItem().toString()));
+ fontStyle.getSelectedIndex(),
+ Integer.parseInt(fontSize.getSelectedItem().toString()));
FontMetrics fm = getGraphics().getFontMetrics(newFont);
- double mw = fm.getStringBounds("M", getGraphics()).getWidth(), iw = fm
- .getStringBounds("I", getGraphics()).getWidth();
+ double mw = fm.getStringBounds("M", getGraphics()).getWidth(),
+ iw = fm.getStringBounds("I", getGraphics()).getWidth();
if (mw < 1 || iw < 1)
{
// TODO: JAL-1100
protected void scaleAsCdna_actionPerformed()
{
ap.av.setScaleProteinAsCdna(scaleAsCdna.getState());
- ap.av.getCodingComplement().setScaleProteinAsCdna(
- scaleAsCdna.getState());
+ ap.av.getCodingComplement()
+ .setScaleProteinAsCdna(scaleAsCdna.getState());
changeFont();
}
ss = es - vertical;
if (ss < ranges.getStartSeq()) // ie scrolling too fast, more than a page
// at a
- // time
+ // time
{
ss = ranges.getStartSeq();
}
// Fill in the background
gg.setColor(Color.white);
- Font italic = new Font(av.getFont().getName(), Font.ITALIC, av
- .getFont().getSize());
+ Font italic = new Font(av.getFont().getName(), Font.ITALIC,
+ av.getFont().getSize());
gg.setFont(italic);
gg.fillRect(0, 0, getSize().width, getSize().height);
continue;
}
// hardwired italic IDs in applet currently
- Font italic = new Font(av.getFont().getName(), Font.ITALIC, av
- .getFont().getSize());
+ Font italic = new Font(av.getFont().getName(), Font.ITALIC,
+ av.getFont().getSize());
gg.setFont(italic);
// boolean isrep=false;
if (doHiddenCheck)
int rowSize = av.getRanges().getViewportWidth();
// hardwired italic IDs in applet currently
- Font italic = new Font(av.getFont().getName(), Font.ITALIC, av
- .getFont().getSize());
+ Font italic = new Font(av.getFont().getName(), Font.ITALIC,
+ av.getFont().getSize());
gg.setFont(italic);
/*
void drawMarker(int i, int starty, int yoffset)
{
- SequenceI[] hseqs = av.getAlignment().getHiddenSequences().hiddenSequences;
+ SequenceI[] hseqs = av.getAlignment()
+ .getHiddenSequences().hiddenSequences;
// Use this method here instead of calling hiddenSeq adjust
// 3 times.
int hSize = hseqs.length;
gg.setColor(Color.blue);
if (below)
{
- gg.fillPolygon(new int[] { getSize().width - avcharHeight,
- getSize().width - avcharHeight, getSize().width }, new int[] {
- (i - starty) * avcharHeight + yoffset,
- (i - starty) * avcharHeight + yoffset + avcharHeight / 4,
- (i - starty) * avcharHeight + yoffset }, 3);
+ gg.fillPolygon(
+ new int[]
+ { getSize().width - avcharHeight,
+ getSize().width - avcharHeight, getSize().width },
+ new int[]
+ { (i - starty) * avcharHeight + yoffset,
+ (i - starty) * avcharHeight + yoffset + avcharHeight / 4,
+ (i - starty) * avcharHeight + yoffset },
+ 3);
}
if (above)
{
- gg.fillPolygon(new int[] { getSize().width - avcharHeight,
- getSize().width - avcharHeight, getSize().width }, new int[] {
- (i - starty + 1) * avcharHeight + yoffset,
- (i - starty + 1) * avcharHeight + yoffset - avcharHeight / 4,
- (i - starty + 1) * avcharHeight + yoffset }, 3);
+ gg.fillPolygon(
+ new int[]
+ { getSize().width - avcharHeight,
+ getSize().width - avcharHeight, getSize().width },
+ new int[]
+ { (i - starty + 1) * avcharHeight + yoffset,
+ (i - starty + 1) * avcharHeight + yoffset
+ - avcharHeight / 4,
+ (i - starty + 1) * avcharHeight + yoffset },
+ 3);
}
}
boolean setHiddenFont(SequenceI seq)
{
- Font bold = new Font(av.getFont().getName(), Font.BOLD, av.getFont()
- .getSize());
+ Font bold = new Font(av.getFont().getName(), Font.BOLD,
+ av.getFont().getSize());
if (av.isReferenceSeq(seq) || av.isHiddenRepSequence(seq))
{
{
String propertyName = evt.getPropertyName();
if (propertyName.equals(ViewportRanges.STARTSEQ)
- || (av.getWrapAlignment() && propertyName
- .equals(ViewportRanges.STARTRES)))
+ || (av.getWrapAlignment()
+ && propertyName.equals(ViewportRanges.STARTRES)))
{
fastPaint((int) evt.getNewValue() - (int) evt.getOldValue());
}
import java.util.HashMap;
import java.util.List;
-public class IdPanel extends Panel implements MouseListener,
- MouseMotionListener
+public class IdPanel extends Panel
+ implements MouseListener, MouseMotionListener
{
protected IdCanvas idCanvas;
}
if (tooltip == null)
{
- tooltip = new Tooltip(sequence.getDisplayId(true) + "\n"
- + tooltiptext.toString(), idCanvas);
+ tooltip = new Tooltip(
+ sequence.getDisplayId(true) + "\n" + tooltiptext.toString(),
+ idCanvas);
}
else
{
- tooltip.setTip(sequence.getDisplayId(true) + "\n"
- + tooltiptext.toString());
+ tooltip.setTip(
+ sequence.getDisplayId(true) + "\n" + tooltiptext.toString());
}
tooltiptext = null;
}
int seq = alignPanel.seqPanel.findSeq(e);
- if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+ if ((e.getModifiers()
+ & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
{
Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq);
}
if ((av.getSelectionGroup() == null)
- || ((!jalview.util.Platform.isControlDown(e) && !e
- .isShiftDown()) && av.getSelectionGroup() != null))
+ || ((!jalview.util.Platform.isControlDown(e)
+ && !e.isShiftDown()) && av.getSelectionGroup() != null))
{
av.setSelectionGroup(new SequenceGroup());
av.getSelectionGroup().setStartRes(0);
}
for (int i = start; i <= end; i++)
{
- av.getSelectionGroup().addSequence(
- av.getAlignment().getSequenceAt(i), i == end);
+ av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
+ i == end);
}
}
import java.awt.event.MouseListener;
import java.awt.event.MouseMotionListener;
-public class IdwidthAdjuster extends Panel implements MouseListener,
- MouseMotionListener
+public class IdwidthAdjuster extends Panel
+ implements MouseListener, MouseMotionListener
{
boolean active = false;
width, height);
}
- public JVDialog(Frame owner, Panel mainPanel, String title,
- boolean modal, int width, int height)
+ public JVDialog(Frame owner, Panel mainPanel, String title, boolean modal,
+ int width, int height)
{
super(owner, title, modal);
this.owner = owner;
setLayout(null);
od = new OverviewDimensionsShowHidden(av.getRanges(),
- (av.isShowAnnotation() && av.getSequenceConsensusHash() != null));
+ (av.isShowAnnotation()
+ && av.getSequenceConsensusHash() != null));
oviewCanvas = new OverviewCanvas(od, av);
setLayout(new BorderLayout());
@Override
public void mouseClicked(MouseEvent evt)
{
- if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+ if ((evt.getModifiers()
+ & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
{
showPopupMenu(evt);
}
@Override
public void mouseDragged(MouseEvent evt)
{
- if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+ if ((evt.getModifiers()
+ & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
{
if (!Platform.isAMac())
{
public void run()
{
oviewCanvas.draw(av.isShowSequenceFeatures(),
- (av.isShowAnnotation() && av
- .getAlignmentConservationAnnotation() != null),
+ (av.isShowAnnotation()
+ && av.getAlignmentConservationAnnotation() != null),
ap.seqPanel.seqCanvas.getFeatureRenderer());
setBoxPosition();
}
*/
private void setBoxPosition()
{
- od.setBoxPosition(av.getAlignment()
-.getHiddenSequences(), av
- .getAlignment().getHiddenColumns());
+ od.setBoxPosition(av.getAlignment().getHiddenSequences(),
+ av.getAlignment().getHiddenColumns());
repaint();
}
{
showHidden = false;
od = new OverviewDimensionsHideHidden(av.getRanges(),
- (av.isShowAnnotation() && av
- .getAlignmentConservationAnnotation() != null));
+ (av.isShowAnnotation()
+ && av.getAlignmentConservationAnnotation() != null));
}
else
{
showHidden = true;
od = new OverviewDimensionsShowHidden(av.getRanges(),
- (av.isShowAnnotation() && av
- .getAlignmentConservationAnnotation() != null));
+ (av.isShowAnnotation()
+ && av.getAlignmentConservationAnnotation() != null));
}
oviewCanvas.resetOviewDims(od);
updateOverviewImage();
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
-public class PCAPanel extends EmbmenuFrame implements Runnable,
- ActionListener, ItemListener
+public class PCAPanel extends EmbmenuFrame
+ implements Runnable, ActionListener, ItemListener
{
RotatableCanvas rc;
}
else
{
- seqs = viewport.getSelectionGroup().getSequencesInOrder(viewport.getAlignment());
+ seqs = viewport.getSelectionGroup()
+ .getSequencesInOrder(viewport.getAlignment());
}
SeqCigar sq[] = seqstrings.getSequences();
int length = sq[0].getWidth();
}
}
- ScoreModelI scoreModel = ScoreModels.getInstance().getDefaultModel(
- !nucleotide);
+ ScoreModelI scoreModel = ScoreModels.getInstance()
+ .getDefaultModel(!nucleotide);
pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
SimilarityParams.SeqSpace);
if (!pcaModel.isNucleotide())
{
pcaModel.setNucleotide(true);
- ScoreModelI scoreModel = ScoreModels.getInstance().getDefaultModel(
- false);
+ ScoreModelI scoreModel = ScoreModels.getInstance()
+ .getDefaultModel(false);
pcaModel.setScoreModel(scoreModel);
new Thread(this).start();
}
if (pcaModel.isNucleotide())
{
pcaModel.setNucleotide(false);
- ScoreModelI scoreModel = ScoreModels.getInstance().getDefaultModel(
- true);
+ ScoreModelI scoreModel = ScoreModels.getInstance()
+ .getDefaultModel(true);
pcaModel.setScoreModel(scoreModel);
new Thread(this).start();
}
if (alAndColsel != null && alAndColsel[0] != null)
{
Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
- AlignFrame af = new AlignFrame(al, av.applet,
- "Original Data for PCA", false);
+ AlignFrame af = new AlignFrame(al, av.applet, "Original Data for PCA",
+ false);
- af.viewport.getAlignment().setHiddenColumns(
- (HiddenColumns) alAndColsel[1]);
+ af.viewport.getAlignment()
+ .setHiddenColumns((HiddenColumns) alAndColsel[1]);
}
}
values.setLabel(MessageManager.getString("label.output_values"));
values.addActionListener(this);
inputData.setLabel(MessageManager.getString("label.input_data"));
- nuclSetting.setLabel(MessageManager
- .getString("label.nucleotide_matrix"));
+ nuclSetting
+ .setLabel(MessageManager.getString("label.nucleotide_matrix"));
nuclSetting.addItemListener(this);
protSetting.setLabel(MessageManager.getString("label.protein_matrix"));
protSetting.addItemListener(this);
}
else
{
- seqs = ap.av.getSelectionGroup().getSequencesInOrder(
- ap.av.getAlignment());
+ seqs = ap.av.getSelectionGroup()
+ .getSequencesInOrder(ap.av.getAlignment());
}
float scores[][] = new float[seqs.length][seqs.length];
if (count > 2)
{
- System.out
- .println("Pairwise alignment scaled similarity score matrix\n");
+ System.out.println(
+ "Pairwise alignment scaled similarity score matrix\n");
for (int i = 0; i < count; i++)
{
- jalview.util.Format.print(System.out, "%s \n", ("" + i) + " "
- + seqs[i].getName());
+ jalview.util.Format.print(System.out, "%s \n",
+ ("" + i) + " " + seqs[i].getName());
}
System.out.println("\n");
{
for (int j = 0; j < i; j++)
{
- jalview.util.Format.print(System.out, "%7.3f", scores[i][j]
- / totscore);
+ jalview.util.Format.print(System.out, "%7.3f",
+ scores[i][j] / totscore);
}
}
textarea.setFont(new java.awt.Font("Monospaced", 0, 12));
textarea.setText("");
viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12));
- viewInEditorButton.setLabel(MessageManager
- .getString("label.view_alignment_editor"));
+ viewInEditorButton.setLabel(
+ MessageManager.getString("label.view_alignment_editor"));
viewInEditorButton.addActionListener(this);
this.add(scrollPane, BorderLayout.CENTER);
scrollPane.add(textarea);
import java.util.Stack;
import java.util.Vector;
-public class RedundancyPanel extends SliderPanel implements Runnable,
- WindowListener
+public class RedundancyPanel extends SliderPanel
+ implements Runnable, WindowListener
{
Stack historyList = new Stack(); // simpler than synching with alignFrame.
applyButton.setVisible(true);
allGroupsCheck.setVisible(false);
- label.setText(MessageManager
- .getString("label.enter_redundancy_threshold"));
+ label.setText(
+ MessageManager.getString("label.enter_redundancy_threshold"));
valueField.setText("100");
slider.setVisibleAmount(1);
redundancy = AlignSeq.computeRedundancyMatrix(originalSequences,
omitHidden, start, end, false);
- label.setText(MessageManager
- .getString("label.enter_redundancy_threshold"));
+ label.setText(
+ MessageManager.getString("label.enter_redundancy_threshold"));
slider.setVisible(true);
applyButton.setEnabled(true);
valueField.setVisible(true);
ap.alignFrame.addHistoryItem(cut);
PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
- .getSequences());
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
}
}
{
ap.av.getHistoryList().remove(command);
ap.alignFrame.updateEditMenuBar();
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
- .getSequences());
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
}
ap.paintAlignment(true);
if (points == null)
{
g.setFont(new Font("Verdana", Font.PLAIN, 18));
- g.drawString(MessageManager.getString("label.calculating_pca")
- + "....", 20, getSize().height / 2);
+ g.drawString(
+ MessageManager.getString("label.calculating_pca") + "....",
+ 20, getSize().height / 2);
}
else
{
for (int i = 0; i < npoint; i++)
{
SequencePoint sp = (SequencePoint) points.elementAt(i);
- int tmp1 = (int) ((sp.coord[0] - centre[0]) * scale + (float) getSize().width / 2.0);
- int tmp2 = (int) ((sp.coord[1] - centre[1]) * scale + (float) getSize().height / 2.0);
+ int tmp1 = (int) ((sp.coord[0] - centre[0]) * scale
+ + (float) getSize().width / 2.0);
+ int tmp2 = (int) ((sp.coord[1] - centre[1]) * scale
+ + (float) getSize().height / 2.0);
if (tmp1 > x1 && tmp1 < x2 && tmp2 > y1 && tmp2 < y2)
{
import java.beans.PropertyChangeEvent;
import java.util.List;
-public class ScalePanel extends Panel implements MouseMotionListener,
- MouseListener, ViewportListenerI
+public class ScalePanel extends Panel
+ implements MouseMotionListener, MouseListener, ViewportListenerI
{
protected int offy = 4;
min = res;
max = res;
- if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+ if ((evt.getModifiers()
+ & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
{
rightMouseButtonPressed(evt, res);
}
PopupMenu pop = new PopupMenu();
if (reveal != null)
{
- MenuItem item = new MenuItem(MessageManager.getString("label.reveal"));
+ MenuItem item = new MenuItem(
+ MessageManager.getString("label.reveal"));
item.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
av.hideColumns(res, res);
- if (av.getSelectionGroup() != null
- && av.getSelectionGroup().getSize() == av.getAlignment()
- .getHeight())
+ if (av.getSelectionGroup() != null && av.getSelectionGroup()
+ .getSize() == av.getAlignment().getHeight())
{
av.setSelectionGroup(null);
}
*/
if (!av.getWrapAlignment())
{
- drawScale(g, av.getRanges().getStartRes(),
- av.getRanges().getEndRes(), getSize().width, getSize().height);
+ drawScale(g, av.getRanges().getStartRes(), av.getRanges().getEndRes(),
+ getSize().width, getSize().height);
}
}
continue;
}
- gg.fillPolygon(new int[] {
- -1 + res * avCharWidth - avcharHeight / 4,
- -1 + res * avCharWidth + avcharHeight / 4,
- -1 + res * avCharWidth }, new int[] { y, y, y + 2 * yOf }, 3);
+ gg.fillPolygon(
+ new int[]
+ { -1 + res * avCharWidth - avcharHeight / 4,
+ -1 + res * avCharWidth + avcharHeight / 4,
+ -1 + res * avCharWidth },
+ new int[]
+ { y, y, y + 2 * yOf }, 3);
}
}
}
{
if (mstring != null)
{
- g.drawString(mstring, mpos * avcharWidth, ypos
- - (avcharHeight / 2));
+ g.drawString(mstring, mpos * avcharWidth,
+ ypos - (avcharHeight / 2));
}
- g.drawLine((mpos * avcharWidth) + (avcharWidth / 2), (ypos + 2)
- - (avcharHeight / 2), (mpos * avcharWidth)
- + (avcharWidth / 2), ypos - 2);
+ g.drawLine((mpos * avcharWidth) + (avcharWidth / 2),
+ (ypos + 2) - (avcharHeight / 2),
+ (mpos * avcharWidth) + (avcharWidth / 2), ypos - 2);
}
}
}
{
int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))
- avcharWidth / 2;
- g.drawString(value + "", x, (ypos + (i * avcharHeight))
- - (avcharHeight / 5));
+ g.drawString(value + "", x,
+ (ypos + (i * avcharHeight)) - (avcharHeight / 5));
}
}
}
if (value != -1)
{
- g.drawString(String.valueOf(value), 0, (ypos + (i * avcharHeight))
- - (avcharHeight / 5));
+ g.drawString(String.valueOf(value), 0,
+ (ypos + (i * avcharHeight)) - (avcharHeight / 5));
}
}
}
lastsr = ranges.getStartRes();
fastPaint = true;
- gg.copyArea(horizontal * avcharWidth, vertical * avcharHeight, imgWidth
- - horizontal * avcharWidth,
+ gg.copyArea(horizontal * avcharWidth, vertical * avcharHeight,
+ imgWidth - horizontal * avcharWidth,
imgHeight - vertical * avcharHeight, -horizontal * avcharWidth,
-vertical * avcharHeight);
- int sr = ranges.getStartRes(), er = ranges.getEndRes(), ss = ranges
- .getStartSeq(), es = ranges
- .getEndSeq(), transX = 0, transY = 0;
+ int sr = ranges.getStartRes(), er = ranges.getEndRes(),
+ ss = ranges.getStartSeq(), es = ranges.getEndSeq(), transX = 0,
+ transY = 0;
if (horizontal > 0) // scrollbar pulled right, image to the left
{
ss = es - vertical;
if (ss < ranges.getStartSeq()) // ie scrolling too fast, more than a page
// at a
- // time
+ // time
{
ss = ranges.getStartSeq();
}
{
if (img != null
- && (fastPaint || (getSize().width != g.getClipBounds().width) || (getSize().height != g
- .getClipBounds().height)))
+ && (fastPaint || (getSize().width != g.getClipBounds().width)
+ || (getSize().height != g.getClipBounds().height)))
{
g.drawImage(img, 0, 0, this);
fastPaint = false;
continue;
}
- gg.fillPolygon(new int[] { res * avcharWidth - avcharHeight / 4,
- res * avcharWidth + avcharHeight / 4, res * avcharWidth },
- new int[] { ypos - (avcharHeight / 2),
- ypos - (avcharHeight / 2),
- ypos - (avcharHeight / 2) + 8 }, 3);
+ gg.fillPolygon(
+ new int[]
+ { res * avcharWidth - avcharHeight / 4,
+ res * avcharWidth + avcharHeight / 4,
+ res * avcharWidth },
+ new int[]
+ { ypos - (avcharHeight / 2), ypos - (avcharHeight / 2),
+ ypos - (avcharHeight / 2) + 8 },
+ 3);
}
}
{
g1.setColor(Color.blue);
g1.drawLine((blockEnd - blockStart + 1) * avcharWidth - 1,
- 0 + offset, (blockEnd - blockStart + 1) * avcharWidth
- - 1, (endSeq - startSeq + 1) * avcharHeight
- + offset);
+ 0 + offset,
+ (blockEnd - blockStart + 1) * avcharWidth - 1,
+ (endSeq - startSeq + 1) * avcharHeight + offset);
}
g1.translate(-screenY * avcharWidth, 0);
if (av.isShowSequenceFeatures())
{
- fr.drawSequence(g, nextSeq, startRes, endRes, offset
- + ((i - startSeq) * avcharHeight), false);
+ fr.drawSequence(g, nextSeq, startRes, endRes,
+ offset + ((i - startSeq) * avcharHeight), false);
}
// / Highlight search Results once all sequences have been drawn
if (av.hasSearchResults())
{
int[] visibleResults = av.getSearchResults().getResults(nextSeq,
- startRes,
- endRes);
+ startRes, endRes);
if (visibleResults != null)
{
for (int r = 0; r < visibleResults.length; r += 2)
{
sr.drawHighlightedText(nextSeq, visibleResults[r],
- visibleResults[r + 1], (visibleResults[r] - startRes)
- * avcharWidth, offset
- + ((i - startSeq) * avcharHeight));
+ visibleResults[r + 1],
+ (visibleResults[r] - startRes) * avcharWidth,
+ offset + ((i - startSeq) * avcharHeight));
}
}
}
{
sx = (group.getStartRes() - startRes) * avcharWidth;
sy = offset + ((i - startSeq) * avcharHeight);
- ex = (((group.getEndRes() + 1) - group.getStartRes()) * avcharWidth) - 1;
+ ex = (((group.getEndRes() + 1) - group.getStartRes())
+ * avcharWidth) - 1;
if (sx + ex < 0 || sx > imgWidth)
{
}
if ((sx <= (endRes - startRes) * avcharWidth)
- && group.getSequences(null).contains(
- av.getAlignment().getSequenceAt(i)))
+ && group.getSequences(null)
+ .contains(av.getAlignment().getSequenceAt(i)))
{
if ((bottom == -1)
- && (i >= alHeight || !group.getSequences(null)
- .contains(
- av.getAlignment().getSequenceAt(i + 1))))
+ && (i >= alHeight || !group.getSequences(null).contains(
+ av.getAlignment().getSequenceAt(i + 1))))
{
bottom = sy + avcharHeight;
}
if (!inGroup)
{
- if (((top == -1) && (i == 0))
- || !group.getSequences(null).contains(
- av.getAlignment().getSequenceAt(i - 1)))
+ if (((top == -1) && (i == 0)) || !group.getSequences(null)
+ .contains(av.getAlignment().getSequenceAt(i - 1)))
{
top = sy;
}
if (editCommand != null && editCommand.getSize() > 0)
{
ap.alignFrame.addHistoryItem(editCommand);
- av.firePropertyChange("alignment", null, av.getAlignment()
- .getSequences());
+ av.firePropertyChange("alignment", null,
+ av.getAlignment().getSequences());
}
startseq = -1;
{
seqCanvas.cursorX += dx;
seqCanvas.cursorY += dy;
- if (av.hasHiddenColumns()
- && !av.getAlignment().getHiddenColumns()
- .isVisible(seqCanvas.cursorX))
+ if (av.hasHiddenColumns() && !av.getAlignment().getHiddenColumns()
+ .isVisible(seqCanvas.cursorX))
{
int original = seqCanvas.cursorX - dx;
int maxWidth = av.getAlignment().getWidth();
while (!av.getAlignment().getHiddenColumns()
- .isVisible(seqCanvas.cursorX)
- && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
+ .isVisible(seqCanvas.cursorX) && seqCanvas.cursorX < maxWidth
+ && seqCanvas.cursorX > 0)
{
seqCanvas.cursorX += dx;
}
- if (seqCanvas.cursorX >= maxWidth
- || !av.getAlignment().getHiddenColumns()
- .isVisible(seqCanvas.cursorX))
+ if (seqCanvas.cursorX >= maxWidth || !av.getAlignment()
+ .getHiddenColumns().isVisible(seqCanvas.cursorX))
{
seqCanvas.cursorX = original;
}
{
ranges.scrollUp(false);
}
- while (seqCanvas.cursorX < hidden.adjustForHiddenColumns(ranges
- .getStartRes()))
+ while (seqCanvas.cursorX < hidden
+ .adjustForHiddenColumns(ranges.getStartRes()))
{
if (!ranges.scrollRight(false))
break;
}
}
- while (seqCanvas.cursorX > hidden.adjustForHiddenColumns(ranges
- .getEndRes()))
+ while (seqCanvas.cursorX > hidden
+ .adjustForHiddenColumns(ranges.getEndRes()))
{
if (!ranges.scrollRight(true))
{
}
else
{
- residue = "X".equalsIgnoreCase(displayChar) ? "X" : ("*"
- .equals(displayChar) ? "STOP" : ResidueProperties.aa2Triplet
- .get(displayChar));
+ residue = "X".equalsIgnoreCase(displayChar) ? "X"
+ : ("*".equals(displayChar) ? "STOP"
+ : ResidueProperties.aa2Triplet.get(displayChar));
if (residue != null)
{
text.append(" Residue: ").append(residue);
// For now, ignore the mouseWheel font resizing on Macs
// As the Button2_mask always seems to be true
- if ((evt.getModifiers() & InputEvent.BUTTON2_MASK) == InputEvent.BUTTON2_MASK
+ if ((evt.getModifiers()
+ & InputEvent.BUTTON2_MASK) == InputEvent.BUTTON2_MASK
&& !av.MAC)
{
mouseWheelPressed = true;
if (!features.isEmpty())
{
SearchResultsI highlight = new SearchResults();
- highlight.addResult(sequence, features.get(0).getBegin(), features
- .get(0).getEnd());
+ highlight.addResult(sequence, features.get(0).getBegin(),
+ features.get(0).getEnd());
seqCanvas.highlightSearchResults(highlight);
seqCanvas.getFeatureRenderer().amendFeatures(
Collections.singletonList(sequence), features, false, ap);
y -= hgap;
- seq = Math.min((y % cHeight) / av.getCharHeight(), av.getAlignment()
- .getHeight() - 1);
+ seq = Math.min((y % cHeight) / av.getCharHeight(),
+ av.getAlignment().getHeight() - 1);
if (seq < 0)
{
seq = -1;
}
else
{
- seq = Math.min((y / av.getCharHeight())
- + av.getRanges().getStartSeq(),
- av
- .getAlignment().getHeight() - 1);
+ seq = Math.min(
+ (y / av.getCharHeight()) + av.getRanges().getStartSeq(),
+ av.getAlignment().getHeight() - 1);
if (seq < 0)
{
seq = -1;
else
{
String residue = (ch == 'x' || ch == 'X') ? "X"
- : ResidueProperties.aa2Triplet
- .get(String.valueOf(ch));
+ : ResidueProperties.aa2Triplet.get(String.valueOf(ch));
text.append(" Residue: ").append(residue == null ? ch : residue);
}
text.append(" (").append(Integer.toString(respos)).append(")");
{
for (int g = 0; g < groups.length; g++)
{
- if (groups[g].getStartRes() <= column && groups[g].getEndRes() >= column)
+ if (groups[g].getStartRes() <= column
+ && groups[g].getEndRes() >= column)
{
if (!groups[g].getName().startsWith("JTreeGroup")
&& !groups[g].getName().startsWith("JGroup"))
{
for (int i = 0; i < features.length; i++)
{
- if (av.getFeaturesDisplayed() == null
- || !av.getFeaturesDisplayed().isVisible(
- features[i].getType()))
+ if (av.getFeaturesDisplayed() == null || !av.getFeaturesDisplayed()
+ .isVisible(features[i].getType()))
{
continue;
}
- if (features[i].featureGroup != null
- && !seqCanvas.fr.checkGroupVisibility(
- features[i].featureGroup, false))
+ if (features[i].featureGroup != null && !seqCanvas.fr
+ .checkGroupVisibility(features[i].featureGroup, false))
{
continue;
}
int oldWidth = av.getCharWidth();
// Which is bigger, left-right or up-down?
- if (Math.abs(evt.getY() - lastMousePress.y) > Math.abs(evt.getX()
- - lastMousePress.x))
+ if (Math.abs(evt.getY() - lastMousePress.y) > Math
+ .abs(evt.getX() - lastMousePress.x))
{
int fontSize = av.font.getSize();
StringBuffer message = new StringBuffer();
if (groupEditing)
{
- message.append(MessageManager.getString("action.edit_group")).append(
- ":");
+ message.append(MessageManager.getString("action.edit_group"))
+ .append(":");
if (editCommand == null)
{
editCommand = new EditCommand(
}
if (editCommand == null)
{
- editCommand = new EditCommand(MessageManager.formatMessage(
- "label.edit_params", new String[] { label }));
+ editCommand = new EditCommand(MessageManager
+ .formatMessage("label.edit_params", new String[]
+ { label }));
}
}
ap.alignFrame.statusBar.setText(message.toString());
// Are we editing within a selection group?
- if (groupEditing
- || (sg != null && sg.getSequences(av.getHiddenRepSequences())
- .contains(seq)))
+ if (groupEditing || (sg != null
+ && sg.getSequences(av.getHiddenRepSequences()).contains(seq)))
{
fixedColumns = true;
{
for (int j = 0; j < startres - lastres; j++)
{
- if (!jalview.util.Comparison.isGap(gs.getCharAt(fixedRight
- - j)))
+ if (!jalview.util.Comparison
+ .isGap(gs.getCharAt(fixedRight - j)))
{
blank = false;
break;
}
else
{
- editCommand.appendEdit(Action.INSERT_GAP,
- new SequenceI[] { seq }, lastres, startres - lastres,
- av.getAlignment(), true);
+ editCommand.appendEdit(Action.INSERT_GAP, new SequenceI[] { seq },
+ lastres, startres - lastres, av.getAlignment(), true);
}
}
else
if (max > 0)
{
editCommand.appendEdit(Action.DELETE_GAP,
- new SequenceI[] { seq }, startres, max,
- av.getAlignment(), true);
+ new SequenceI[]
+ { seq }, startres, max, av.getAlignment(), true);
}
}
}
}
// DETECT RIGHT MOUSE BUTTON IN AWT
- if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+ if ((evt.getModifiers()
+ & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
{
List<SequenceFeature> allFeatures = findFeaturesAtRes(sequence,
sequence.findPosition(res));
running = av.getRanges().scrollUp(true);
}
- if (mouseDragging && evt.getY() >= getSize().height
- && av.getAlignment().getHeight() > av.getRanges()
- .getEndSeq())
+ if (mouseDragging && evt.getY() >= getSize().height && av
+ .getAlignment().getHeight() > av.getRanges().getEndSeq())
{
running = av.getRanges().scrollUp(false);
}
// handles selection messages...
// TODO: extend config options to allow user to control if selections may be
// shared between viewports.
- if (av != null
- && (av == source || !av.followSelection || (source instanceof AlignViewport && ((AlignmentViewport) source)
- .getSequenceSetId().equals(av.getSequenceSetId()))))
+ if (av != null && (av == source || !av.followSelection
+ || (source instanceof AlignViewport
+ && ((AlignmentViewport) source).getSequenceSetId()
+ .equals(av.getSequenceSetId()))))
{
return;
}
{
if (av.getAlignment() == null)
{
- System.out
- .println("Selection message: alignviewport av SeqSetId="
- + av.getSequenceSetId() + " ViewId="
- + av.getViewId()
- + " 's alignment is NULL! returning immediatly.");
+ System.out.println("Selection message: alignviewport av SeqSetId="
+ + av.getSequenceSetId() + " ViewId=" + av.getViewId()
+ + " 's alignment is NULL! returning immediatly.");
return;
}
sgroup = seqsel.intersect(av.getAlignment(),
}
repaint = av.isSelectionGroupChanged(true);
}
- if (copycolsel
- && (av.getColumnSelection() == null || !av
- .isColSelChanged(true)))
+ if (copycolsel && (av.getColumnSelection() == null
+ || !av.isColSelChanged(true)))
{
// the current selection is unset or from a previous message
// so import the new colsel.
}
repaint |= av.isColSelChanged(true);
}
- if (copycolsel
- && av.hasHiddenColumns()
+ if (copycolsel && av.hasHiddenColumns()
&& (av.getColumnSelection() == null))
{
System.err.println("Bad things");
{
row = row < 0 ? ap.av.getRanges().getStartSeq() : row;
- ap.scrollTo(ap.av.getRanges().getStartRes(), ap.av.getRanges()
- .getStartRes(), row, true, true);
+ ap.scrollTo(ap.av.getRanges().getStartRes(),
+ ap.av.getRanges().getStartRes(), row, true, true);
}
/**
{
column = column < 0 ? ap.av.getRanges().getStartRes() : column;
- ap.scrollTo(column, column, ap.av.getRanges().getStartSeq(), true, true);
+ ap.scrollTo(column, column, ap.av.getRanges().getStartSeq(), true,
+ true);
}
/**
int length = seq.getLength();
int curStart = -1;
- int curWidth = av.getCharWidth(), avCharWidth = av.getCharWidth(), avCharHeight = av
- .getCharHeight();
+ int curWidth = av.getCharWidth(), avCharWidth = av.getCharWidth(),
+ avCharHeight = av.getCharHeight();
Color tempColour = null;
while (i <= end)
}
charOffset = (avCharWidth - fm.charWidth(s)) / 2;
- graphics.drawString(String.valueOf(s), charOffset + avCharWidth
- * (i - start), y1);
+ graphics.drawString(String.valueOf(s),
+ charOffset + avCharWidth * (i - start), y1);
}
}
// currentSequenceGroup.getConsensus()
char conschar = (usesrep) ? (currentGroup == null
|| position < currentGroup.getStartRes()
- || position > currentGroup.getEndRes() ? av.getAlignment()
- .getSeqrep().getCharAt(position)
- : (currentGroup.getSeqrep() != null ? currentGroup.getSeqrep()
- .getCharAt(position) : av.getAlignment().getSeqrep()
- .getCharAt(position)))
+ || position > currentGroup.getEndRes()
+ ? av.getAlignment().getSeqrep().getCharAt(position)
+ : (currentGroup.getSeqrep() != null
+ ? currentGroup.getSeqrep().getCharAt(position)
+ : av.getAlignment().getSeqrep()
+ .getCharAt(position)))
: (currentGroup != null && currentGroup.getConsensus() != null
&& position >= currentGroup.getStartRes()
- && position <= currentGroup.getEndRes() && currentGroup
- .getConsensus().annotations.length > position) ? currentGroup
- .getConsensus().annotations[position].displayCharacter
- .charAt(0)
- : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
- .charAt(0);
+ && position <= currentGroup.getEndRes()
+ && currentGroup
+ .getConsensus().annotations.length > position)
+ ? currentGroup
+ .getConsensus().annotations[position].displayCharacter
+ .charAt(0)
+ : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
+ .charAt(0);
if (!jalview.util.Comparison.isGap(conschar)
- && (sequenceChar == conschar || sequenceChar + CHAR_TO_UPPER == conschar))
+ && (sequenceChar == conschar
+ || sequenceChar + CHAR_TO_UPPER == conschar))
{
sequenceChar = conservedChar;
}
return false;
}
- public void drawHighlightedText(SequenceI seq, int start, int end,
- int x1, int y1)
+ public void drawHighlightedText(SequenceI seq, int start, int end, int x1,
+ int y1)
{
int avCharWidth = av.getCharWidth(), avCharHeight = av.getCharHeight();
int pady = avCharHeight / 5;
int charOffset = 0;
graphics.setColor(Color.black);
- graphics.fillRect(x1, y1, avCharWidth * (end - start + 1), avCharHeight);
+ graphics.fillRect(x1, y1, avCharWidth * (end - start + 1),
+ avCharHeight);
graphics.setColor(Color.white);
char s = '~';
}
charOffset = (avCharWidth - fm.charWidth(s)) / 2;
- graphics.drawString(String.valueOf(s), charOffset + x1
- + avCharWidth * (i - start), y1 + avCharHeight - pady);
+ graphics.drawString(String.valueOf(s),
+ charOffset + x1 + avCharWidth * (i - start),
+ y1 + avCharHeight - pady);
}
}
}
import java.awt.event.WindowEvent;
import java.util.List;
-public class SliderPanel extends Panel implements ActionListener,
- AdjustmentListener, MouseListener
+public class SliderPanel extends Panel
+ implements ActionListener, AdjustmentListener, MouseListener
{
private static final String BACKGROUND = "Background";
}
conservationSlider.setTitle(MessageManager.formatMessage(
- "label.conservation_colour_increment",
- new String[] { source == null ? BACKGROUND : source }));
+ "label.conservation_colour_increment", new String[]
+ { source == null ? BACKGROUND : source }));
List<SequenceGroup> groups = ap.av.getAlignment().getGroups();
if (groups != null && !groups.isEmpty())
{
pid.valueField.setText(String.valueOf(ccs.getThreshold()));
}
PIDSlider.setTitle(MessageManager.formatMessage(
- "label.percentage_identity_threshold",
- new String[] { source == null ? BACKGROUND : source }));
+ "label.percentage_identity_threshold", new String[]
+ { source == null ? BACKGROUND : source }));
if (ap.av.getAlignment().getGroups() != null)
{
if (!PIDSlider.isVisible())
{
- jalview.bin.JalviewLite.addFrame(PIDSlider, PIDSlider.getTitle(),
- 420, 100);
+ jalview.bin.JalviewLite.addFrame(PIDSlider, PIDSlider.getTitle(), 420,
+ 100);
PIDSlider.addWindowListener(new WindowAdapter()
{
@Override
conservationSlider = null;
}
}
+
public SliderPanel(AlignmentPanel ap, int value, boolean forConserve,
ResidueShaderI shader)
{
valueChanged(slider.getValue());
}
});
-
+
label.setFont(new java.awt.Font("Verdana", 0, 11));
label.setText(MessageManager.getString("label.set_this_label_text"));
jPanel1.setLayout(borderLayout1);
undoButton.addActionListener(this);
allGroupsCheck.setEnabled(false);
allGroupsCheck.setFont(new java.awt.Font("Verdana", 0, 11));
- allGroupsCheck.setLabel(MessageManager
- .getString("action.apply_threshold_all_groups"));
- allGroupsCheck.setName(MessageManager
- .getString("action.apply_all_groups"));
+ allGroupsCheck.setLabel(
+ MessageManager.getString("action.apply_threshold_all_groups"));
+ allGroupsCheck
+ .setName(MessageManager.getString("action.apply_all_groups"));
this.setBackground(Color.white);
this.setForeground(Color.black);
jPanel2.add(label, null);
* Compute cDNA consensus on protein alignment
*/
protein.initComplementConsensus();
- AlignmentViewPanel ap = topAlignment.isNucleotide() ? bottomFrame.alignPanel
+ AlignmentViewPanel ap = topAlignment.isNucleotide()
+ ? bottomFrame.alignPanel
: topFrame.alignPanel;
protein.updateConsensus(ap);
{
AlignmentViewport cdna = topFrame.getAlignViewport().getAlignment()
.isNucleotide() ? topFrame.viewport : bottomFrame.viewport;
- AlignmentViewport protein = cdna == topFrame.viewport ? bottomFrame.viewport
+ AlignmentViewport protein = cdna == topFrame.viewport
+ ? bottomFrame.viewport
: topFrame.viewport;
/*
if (w1 != w3)
{
Dimension d = topFrame.alignPanel.idPanel.idCanvas.getSize();
- topFrame.alignPanel.idPanel.idCanvas.setSize(new Dimension(w3,
- d.height));
+ topFrame.alignPanel.idPanel.idCanvas
+ .setSize(new Dimension(w3, d.height));
}
if (w2 != w3)
{
Dimension d = bottomFrame.alignPanel.idPanel.idCanvas.getSize();
- bottomFrame.alignPanel.idPanel.idCanvas.setSize(new Dimension(w3,
- d.height));
+ bottomFrame.alignPanel.idPanel.idCanvas
+ .setSize(new Dimension(w3, d.height));
}
/*
private void addAlignFrameComponents(AlignFrame af, Panel panel)
{
panel.setLayout(new BorderLayout());
- Panel menuPanel = af
- .makeEmbeddedPopupMenu(af.getMenuBar(), true, false);
+ Panel menuPanel = af.makeEmbeddedPopupMenu(af.getMenuBar(), true,
+ false);
panel.add(menuPanel, BorderLayout.NORTH);
panel.add(af.statusBar, BorderLayout.SOUTH);
panel.add(af.alignPanel, BorderLayout.CENTER);
this.add(outermost);
int width = Math.max(topFrame.frameWidth, bottomFrame.frameWidth);
int height = topFrame.frameHeight + bottomFrame.frameHeight;
- jalview.bin.JalviewLite
- .addFrame(this, this.getTitle(), width, height);
+ jalview.bin.JalviewLite.addFrame(this, this.getTitle(), width,
+ height);
}
}
import java.awt.event.MouseMotionListener;
import java.util.StringTokenizer;
-public class Tooltip extends Canvas implements MouseListener,
- MouseMotionListener
+public class Tooltip extends Canvas
+ implements MouseListener, MouseMotionListener
{
private String[] tip;
{
if (lindex > 0)
{
- g.drawString(tip[i].substring(0, lindex), 3, (i + 1) * fontHeight
- - 3);
+ g.drawString(tip[i].substring(0, lindex), 3,
+ (i + 1) * fontHeight - 3);
x += fm.stringWidth(tip[i].substring(0, lindex) + 3);
}
g.drawImage(linkImage, x, i * fontHeight + 1, this);
return;
}
setLocation(
- (owner.getLocationOnScreen().x - mainContainer.getLocationOnScreen().x)
- + evt.getX(),
+ (owner.getLocationOnScreen().x
+ - mainContainer.getLocationOnScreen().x) + evt.getX(),
(owner.getLocationOnScreen().y
- - mainContainer.getLocationOnScreen().y + VERTICAL_OFFSET)
- + evt.getY());
+ - mainContainer.getLocationOnScreen().y
+ + VERTICAL_OFFSET) + evt.getY());
// correction, whole tool tip must be visible
if (mainContainer.getSize().width < (getLocation().x + getSize().width))
import java.util.List;
import java.util.Vector;
-public class TreeCanvas extends Panel implements MouseListener,
- MouseMotionListener
+public class TreeCanvas extends Panel
+ implements MouseListener, MouseMotionListener
{
TreeModel tree;
g.drawString(nodeLabel, xstart + 2, ypos - 2);
}
- String name = (markPlaceholders && node.isPlaceholder()) ? (PLACEHOLDER + node
- .getName()) : node.getName();
+ String name = (markPlaceholders && node.isPlaceholder())
+ ? (PLACEHOLDER + node.getName())
+ : node.getName();
FontMetrics fm = g.getFontMetrics(font);
int charWidth = fm.stringWidth(name) + 3;
int charHeight = fm.getHeight();
g.fillRect(xend - 2, ypos - 2, 4, 4);
}
- int ystart = (int) (node.left() == null ? 0 : (((SequenceNode) node
- .left()).ycount * chunk))
- + offy;
- int yend = (int) (node.right() == null ? 0 : (((SequenceNode) node
- .right()).ycount * chunk)) + offy;
+ int ystart = (int) (node.left() == null ? 0
+ : (((SequenceNode) node.left()).ycount * chunk)) + offy;
+ int yend = (int) (node.right() == null ? 0
+ : (((SequenceNode) node.right()).ycount * chunk)) + offy;
Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);
nodeHash.put(node, pos);
g.setColor(Color.gray);
}
- int x = (int) (threshold * (getSize().width - labelLength - 2 * offx) + offx);
+ int x = (int) (threshold * (getSize().width - labelLength - 2 * offx)
+ + offx);
g.drawLine(x, 0, x, getSize().height);
}
}
else
{
- cs = ColourSchemeProperty.getColourScheme(sg,
- ColourSchemeProperty.getColourName(av
- .getGlobalColourScheme()));
+ cs = ColourSchemeProperty.getColourScheme(sg, ColourSchemeProperty
+ .getColourName(av.getGlobalColourScheme()));
}
// cs is null if shading is an annotationColourGradient
// if (cs != null)
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
-public class TreePanel extends EmbmenuFrame implements ActionListener,
- ItemListener
+public class TreePanel extends EmbmenuFrame
+ implements ActionListener, ItemListener
{
SequenceI[] seq;
AlignFrame af = new AlignFrame(al, av.applet,
"Original Data for Tree", false);
- af.viewport.getAlignment().setHiddenColumns(
- (HiddenColumns) alAndColsel[1]);
+ af.viewport.getAlignment()
+ .setHiddenColumns((HiddenColumns) alAndColsel[1]);
}
}
else
ScoreModelI sm1 = ScoreModels.getInstance().getScoreModel(pwtype,
treeCanvas.ap);
ScoreModelI sm = sm1;
- TreeBuilder njtree = type.equals(TreeBuilder.NEIGHBOUR_JOINING) ? new NJTree(
- av, sm, SimilarityParams.Jalview)
+ TreeBuilder njtree = type.equals(TreeBuilder.NEIGHBOUR_JOINING)
+ ? new NJTree(av, sm, SimilarityParams.Jalview)
: new AverageDistanceTree(av, sm, SimilarityParams.Jalview);
tree = new TreeModel(njtree);
}
bootstrapMenu.setState(showBoots);
treeCanvas.setShowBootstrap(showBoots);
treeCanvas.setShowDistances(showDist);
- treeCanvas.setMarkPlaceholders(av.applet.getDefaultParameter(
- "showUnlinkedTreeNodes", false));
+ treeCanvas.setMarkPlaceholders(av.applet
+ .getDefaultParameter("showUnlinkedTreeNodes", false));
}
treeCanvas.repaint();
jMenu2.setLabel(MessageManager.getString("action.view"));
fontSize.setLabel(MessageManager.getString("action.font"));
fontSize.addActionListener(this);
- bootstrapMenu.setLabel(MessageManager
- .getString("label.show_bootstrap_values"));
+ bootstrapMenu.setLabel(
+ MessageManager.getString("label.show_bootstrap_values"));
bootstrapMenu.addItemListener(this);
distanceMenu.setLabel(MessageManager.getString("label.show_distances"));
distanceMenu.addItemListener(this);
- placeholdersMenu.setLabel(MessageManager
- .getString("label.mark_unassociated_leaves"));
+ placeholdersMenu.setLabel(
+ MessageManager.getString("label.mark_unassociated_leaves"));
placeholdersMenu.addItemListener(this);
fitToWindow.setState(true);
fitToWindow.setLabel(MessageManager.getString("label.fit_to_window"));
import java.awt.event.MouseEvent;
import java.util.Vector;
-public class UserDefinedColours extends Panel implements ActionListener,
- AdjustmentListener, FocusListener
+public class UserDefinedColours extends Panel
+ implements ActionListener, AdjustmentListener, FocusListener
{
AlignmentPanel ap;
// // not 1.1 compatible!
// dialog = new Dialog(((JVDialog)alignframe), title, true);
// } else {
- throw new Error(
- MessageManager
- .getString("label.error_unsupported_owwner_user_colour_scheme"));
+ throw new Error(MessageManager.getString(
+ "label.error_unsupported_owwner_user_colour_scheme"));
}
dialog.add(this);
int height = 160 + alignframe.getInsets().top + getInsets().bottom;
int width = 400;
- dialog.setBounds(alignframe.getBounds().x
- + (alignframe.getSize().width - width) / 2,
+ dialog.setBounds(
+ alignframe.getBounds().x
+ + (alignframe.getSize().width - width) / 2,
alignframe.getBounds().y
- + (alignframe.getSize().height - height) / 2, width,
- height);
+ + (alignframe.getSize().height - height) / 2,
+ width, height);
}
* <li>SHOW_FULLSCREEN boolean</li>
* <li>FONT_NAME java font name for alignment text display</li>
* <li>FONT_SIZE size of displayed alignment text</li>
- * <li>FONT_STYLE style of font displayed (sequence labels are always italic)</li>
+ * <li>FONT_STYLE style of font displayed (sequence labels are always
+ * italic)</li>
* <li>GAP_SYMBOL character to treat as gap symbol (usually -,.,' ')</li>
* <li>LAST_DIRECTORY last directory for browsing alignment</li>
* <li>USER_DEFINED_COLOURS list of user defined colour scheme files</li>
* Sifts settings
*/
public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
- .getProperty("user.home")
- + File.separatorChar
+ .getProperty("user.home") + File.separatorChar
+ ".sifts_downloads" + File.separatorChar;
private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
Logger lcastor = Logger.getLogger("org.exolab.castor");
jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
- laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level",
- Level.INFO.toString())));
+ laxis.setLevel(Level.toLevel(
+ Cache.getDefault("logs.Axis.Level", Level.INFO.toString())));
lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
Level.INFO.toString())));
lcastor = Logger.getLogger("org.exolab.castor.xml");
// lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
// lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
// Level.INFO.toString())));
- jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault(
- "logs.Jalview.level", Level.INFO.toString())));
+ jalview.bin.Cache.log.setLevel(Level.toLevel(Cache
+ .getDefault("logs.Jalview.level", Level.INFO.toString())));
// laxis.addAppender(ap);
// lcastor.addAppender(ap);
// jalview.bin.Cache.log.addAppender(ap);
try
{
fis = new java.net.URL(propertiesFile).openStream();
- System.out.println("Loading jalview properties from : "
- + propertiesFile);
- System.out
- .println("Disabling Jalview writing to user's local properties file.");
+ System.out.println(
+ "Loading jalview properties from : " + propertiesFile);
+ System.out.println(
+ "Disabling Jalview writing to user's local properties file.");
propsAreReadOnly = true;
} catch (Exception ex)
if (getDefault("USE_PROXY", false))
{
- String proxyServer = getDefault("PROXY_SERVER", ""), proxyPort = getDefault(
- "PROXY_PORT", "8080");
+ String proxyServer = getDefault("PROXY_SERVER", ""),
+ proxyPort = getDefault("PROXY_PORT", "8080");
System.out.println("Using proxyServer: " + proxyServer
+ " proxyPort: " + proxyPort);
// LOAD THE AUTHORS FROM THE authors.props file
try
{
- String authorDetails = "jar:".concat(Cache.class
- .getProtectionDomain().getCodeSource().getLocation()
- .toString().concat("!/authors.props"));
+ String authorDetails = "jar:"
+ .concat(Cache.class.getProtectionDomain().getCodeSource()
+ .getLocation().toString().concat("!/authors.props"));
java.net.URL localJarFileURL = new java.net.URL(authorDetails);
SiftsSettings
.setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
- SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache.getDefault(
- "sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
+ SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache
+ .getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
- SiftsSettings.setFailSafePIDThreshold(jalview.bin.Cache.getDefault(
- "sifts_fail_safe_pid_threshold",
- DEFAULT_FAIL_SAFE_PID_THRESHOLD));
+ SiftsSettings.setFailSafePIDThreshold(
+ jalview.bin.Cache.getDefault("sifts_fail_safe_pid_threshold",
+ DEFAULT_FAIL_SAFE_PID_THRESHOLD));
- SiftsSettings.setCacheThresholdInDays(jalview.bin.Cache.getDefault(
- "sifts_cache_threshold_in_days",
- DEFAULT_CACHE_THRESHOLD_IN_DAYS));
+ SiftsSettings.setCacheThresholdInDays(
+ jalview.bin.Cache.getDefault("sifts_cache_threshold_in_days",
+ DEFAULT_CACHE_THRESHOLD_IN_DAYS));
IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
"http://www.jalview.org/services/identifiers"));
// "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
// jnlpVersion will be null if we're using InstallAnywhere
// Dont do this check if running in headless mode
- if (jnlpVersion == null
- && getDefault("VERSION_CHECK", true)
+ if (jnlpVersion == null && getDefault("VERSION_CHECK", true)
&& (System.getProperty("java.awt.headless") == null || System
.getProperty("java.awt.headless").equals("false")))
{
{
System.setProperty("sun.net.client.defaultConnectTimeout",
"5000");
- java.net.URL url = new java.net.URL(Cache.getDefault(
- "www.jalview.org", "http://www.jalview.org")
+ java.net.URL url = new java.net.URL(Cache
+ .getDefault("www.jalview.org", "http://www.jalview.org")
+ "/webstart/jalview.jnlp");
- BufferedReader in = new BufferedReader(new InputStreamReader(
- url.openStream()));
+ BufferedReader in = new BufferedReader(
+ new InputStreamReader(url.openStream()));
String line = null;
while ((line = in.readLine()) != null)
{
}
} catch (Exception ex)
{
- System.out
- .println("Non-fatal exception when checking version at www.jalview.org :");
+ System.out.println(
+ "Non-fatal exception when checking version at www.jalview.org :");
System.out.println(ex);
remoteVersion = getProperty("VERSION");
}
}
} catch (Exception ex)
{
- System.out.println("Error setting property: " + key + " " + obj
- + "\n" + ex);
+ System.out.println(
+ "Error setting property: " + key + " " + obj + "\n" + ex);
}
return obj;
}
{
try
{
- if (jalview.jbgui.GDesktop.class.getClassLoader().loadClass(
- "uk.ac.vamsas.client.VorbaId") != null)
+ if (jalview.jbgui.GDesktop.class.getClassLoader()
+ .loadClass("uk.ac.vamsas.client.VorbaId") != null)
{
- jalview.bin.Cache.log
- .debug("Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
+ jalview.bin.Cache.log.debug(
+ "Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
vamsasJarsArePresent = 1;
Logger lvclient = Logger.getLogger("uk.ac.vamsas");
- lvclient.setLevel(Level.toLevel(Cache.getDefault(
- "logs.Vamsas.Level", Level.INFO.toString())));
+ lvclient.setLevel(Level.toLevel(Cache
+ .getDefault("logs.Vamsas.Level", Level.INFO.toString())));
lvclient.addAppender(log.getAppender("JalviewLogger"));
// Tell the user that debug is enabled
{
try
{
- if (Cache.class.getClassLoader().loadClass(
- "groovy.lang.GroovyObject") != null)
+ if (Cache.class.getClassLoader()
+ .loadClass("groovy.lang.GroovyObject") != null)
{
- jalview.bin.Cache.log
- .debug("Found Groovy (groovy.lang.GroovyObject can be loaded)");
+ jalview.bin.Cache.log.debug(
+ "Found Groovy (groovy.lang.GroovyObject can be loaded)");
groovyJarsArePresent = 1;
Logger lgclient = Logger.getLogger("groovy");
- lgclient.setLevel(Level.toLevel(Cache.getDefault(
- "logs.Groovy.Level", Level.INFO.toString())));
+ lgclient.setLevel(Level.toLevel(Cache
+ .getDefault("logs.Groovy.Level", Level.INFO.toString())));
lgclient.addAppender(log.getAppender("JalviewLogger"));
// Tell the user that debug is enabled
// try to get the tracker class
try
{
- jgoogleanalyticstracker = Cache.class
- .getClassLoader()
- .loadClass(
- "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
- trackerfocus = Cache.class.getClassLoader().loadClass(
- "com.boxysystems.jgoogleanalytics.FocusPoint");
+ jgoogleanalyticstracker = Cache.class.getClassLoader().loadClass(
+ "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
+ trackerfocus = Cache.class.getClassLoader()
+ .loadClass("com.boxysystems.jgoogleanalytics.FocusPoint");
} catch (Exception e)
{
- log.debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
+ log.debug(
+ "com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
tracker = null;
jgoogleanalyticstracker = null;
trackerfocus = null;
try
{
// Google analytics tracking code for Library Finder
- tracker = jgoogleanalyticstracker.getConstructor(
- new Class[] { String.class, String.class, String.class })
- .newInstance(
- new Object[] {
- "Jalview Desktop",
- (vrs = jalview.bin.Cache.getProperty("VERSION")
- + "_"
- + jalview.bin.Cache.getDefault(
- "BUILD_DATE", "unknown")),
- "UA-9060947-1" });
- jgoogleanalyticstracker.getMethod("trackAsynchronously",
- new Class[] { trackerfocus }).invoke(
- tracker,
- new Object[] { trackerfocus.getConstructor(
- new Class[] { String.class }).newInstance(
- new Object[] { "Application Started." }) });
+ tracker = jgoogleanalyticstracker
+ .getConstructor(new Class[]
+ { String.class, String.class, String.class })
+ .newInstance(new Object[]
+ { "Jalview Desktop",
+ (vrs = jalview.bin.Cache.getProperty("VERSION") + "_"
+ + jalview.bin.Cache.getDefault("BUILD_DATE",
+ "unknown")),
+ "UA-9060947-1" });
+ jgoogleanalyticstracker
+ .getMethod("trackAsynchronously", new Class[]
+ { trackerfocus })
+ .invoke(tracker, new Object[]
+ { trackerfocus.getConstructor(new Class[] { String.class })
+ .newInstance(new Object[]
+ { "Application Started." }) });
} catch (RuntimeException e)
{
re = e;
{
if (re != null)
{
- log.debug("Caught runtime exception in googletracker init:", re);
+ log.debug("Caught runtime exception in googletracker init:",
+ re);
}
if (ex != null)
{
log.warn(
"Failed to initialise GoogleTracker for Jalview Desktop with version "
- + vrs, ex);
+ + vrs,
+ ex);
}
if (err != null)
{
log.error(
"Whilst initing GoogleTracker for Jalview Desktop version "
- + vrs, err);
+ + vrs,
+ err);
}
}
else
{
if (re != null)
{
- System.err
- .println("Debug: Caught runtime exception in googletracker init:"
+ System.err.println(
+ "Debug: Caught runtime exception in googletracker init:"
+ vrs);
re.printStackTrace();
}
if (ex != null)
{
- System.err
- .println("Warning: Failed to initialise GoogleTracker for Jalview Desktop with version "
+ System.err.println(
+ "Warning: Failed to initialise GoogleTracker for Jalview Desktop with version "
+ vrs);
ex.printStackTrace();
}
if (err != null)
{
- System.err
- .println("ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
+ System.err.println(
+ "ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
+ vrs);
err.printStackTrace();
}
{
return;
}
-
+
// In case colours can't be loaded, we'll remove them
// from the default list here.
StringBuffer coloursFound = new StringBuffer();
{
if (coloursFound.toString().length() > 1)
{
- setProperty(UserDefinedColours.USER_DEFINED_COLOURS, coloursFound.toString());
+ setProperty(UserDefinedColours.USER_DEFINED_COLOURS,
+ coloursFound.toString());
}
else
{
- applicationProperties.remove(UserDefinedColours.USER_DEFINED_COLOURS);
+ applicationProperties
+ .remove(UserDefinedColours.USER_DEFINED_COLOURS);
}
}
}
void doMain(String[] args)
{
System.setSecurityManager(null);
- System.out.println("Java version: "
- + System.getProperty("java.version"));
+ System.out
+ .println("Java version: " + System.getProperty("java.version"));
System.out.println(System.getProperty("os.arch") + " "
+ System.getProperty("os.name") + " "
+ System.getProperty("os.version"));
Cache.loadProperties(usrPropsFile); // must do this before
if (usrPropsFile != null)
{
- System.out.println("CMD [-props " + usrPropsFile
- + "] executed successfully!");
+ System.out.println(
+ "CMD [-props " + usrPropsFile + "] executed successfully!");
}
// anything else!
try
{
Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
- System.out.println("CMD [-jabaws " + jabawsUrl
- + "] executed successfully!");
+ System.out.println(
+ "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
} catch (MalformedURLException e)
{
- System.err.println("Invalid jabaws parameter: " + jabawsUrl
- + " ignored");
+ System.err.println(
+ "Invalid jabaws parameter: " + jabawsUrl + " ignored");
}
}
} catch (NoClassDefFoundError error)
{
error.printStackTrace();
- System.out
- .println("\nEssential logging libraries not found."
- + "\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview");
+ System.out.println("\nEssential logging libraries not found."
+ + "\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview");
System.exit(0);
}
System.setProperty("apple.laf.useScreenMenuBar", "true");
try
{
- UIManager.setLookAndFeel(ch.randelshofer.quaqua.QuaquaManager
- .getLookAndFeel());
+ UIManager.setLookAndFeel(
+ ch.randelshofer.quaqua.QuaquaManager.getLookAndFeel());
} catch (Throwable e)
{
- System.err.println("Failed to set QuaQua look and feel: "
- + e.toString());
+ System.err.println(
+ "Failed to set QuaQua look and feel: " + e.toString());
}
}
// questionnaire
Cache.log.debug("Starting questionnaire url at " + url);
desktop.checkForQuestionnaire(url);
- System.out.println("CMD questionnaire[-" + url
- + "] executed successfully!");
+ System.out.println(
+ "CMD questionnaire[-" + url + "] executed successfully!");
}
else
{
// "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
// //
String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
- Cache.log.debug("Starting questionnaire with default url: "
- + defurl);
+ Cache.log.debug(
+ "Starting questionnaire with default url: " + defurl);
desktop.checkForQuestionnaire(defurl);
}
}
{
if (desktop == null || headless)
{
- System.out
- .println("Headless vamsas sessions not yet supported. Sorry.");
+ System.out.println(
+ "Headless vamsas sessions not yet supported. Sorry.");
System.exit(1);
}
// if we have a file, start a new session and import it.
{
if (desktop.joinVamsasSession(vamsasSession))
{
- System.out.println("Successfully joined vamsas session "
- + vamsasSession);
+ System.out.println(
+ "Successfully joined vamsas session " + vamsasSession);
}
else
{
}
} catch (Exception e)
{
- System.err.println("ERROR: Failed to join vamsas session "
- + vamsasSession);
+ System.err.println(
+ "ERROR: Failed to join vamsas session " + vamsasSession);
e.printStackTrace();
}
if (vamsasImport != null)
{
// the Jalview specific remnants can now be imported into the new
// session at the user's leisure.
- Cache.log
- .info("Skipping Push for import of data into existing vamsas session."); // TODO:
+ Cache.log.info(
+ "Skipping Push for import of data into existing vamsas session."); // TODO:
// enable
// this
// when
{
if (!headless)
{
- desktop.setProgressBar(MessageManager
- .getString("status.processing_commandline_args"),
+ desktop.setProgressBar(
+ MessageManager
+ .getString("status.processing_commandline_args"),
progress = System.currentTimeMillis());
}
System.out.println("CMD [-open " + file + "] executed successfully!");
{
data.replaceAll("%20", " ");
- ColourSchemeI cs = ColourSchemeProperty.getColourScheme(af
- .getViewport().getAlignment(), data);
+ ColourSchemeI cs = ColourSchemeProperty
+ .getColourScheme(af.getViewport().getAlignment(), data);
if (cs != null)
{
- System.out.println("CMD [-color " + data
- + "] executed successfully!");
+ System.out.println(
+ "CMD [-color " + data + "] executed successfully!");
}
af.changeColour(cs);
}
af.parseFeaturesFile(data,
AppletFormatAdapter.checkProtocol(data));
// System.out.println("Added " + data);
- System.out.println("CMD groups[-" + data
- + "] executed successfully!");
+ System.out.println(
+ "CMD groups[-" + data + "] executed successfully!");
}
data = aparser.getValue("features", true);
if (data != null)
af.parseFeaturesFile(data,
AppletFormatAdapter.checkProtocol(data));
// System.out.println("Added " + data);
- System.out.println("CMD [-features " + data
- + "] executed successfully!");
+ System.out.println(
+ "CMD [-features " + data + "] executed successfully!");
}
data = aparser.getValue("annotations", true);
{
af.loadJalviewDataFile(data, null, null, null);
// System.out.println("Added " + data);
- System.out.println("CMD [-annotations " + data
- + "] executed successfully!");
+ System.out.println(
+ "CMD [-annotations " + data + "] executed successfully!");
}
// set or clear the sortbytree flag.
if (aparser.contains("sortbytree"))
{
try
{
- System.out.println("CMD [-tree " + data
- + "] executed successfully!");
+ System.out.println(
+ "CMD [-tree " + data + "] executed successfully!");
NewickFile nf = new NewickFile(data,
AppletFormatAdapter.checkProtocol(data));
- af.getViewport().setCurrentTree(
- af.showNewickTree(nf, data).getTree());
+ af.getViewport()
+ .setCurrentTree(af.showNewickTree(nf, data).getTree());
} catch (IOException ex)
{
System.err.println("Couldn't add tree " + data);
}
try
{
- BioJsHTMLOutput
- .refreshVersionInfo(BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+ BioJsHTMLOutput.refreshVersionInfo(
+ BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
} catch (URISyntaxException e)
{
e.printStackTrace();
}
BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
bjs.exportHTML(file);
- System.out.println("Creating BioJS MSA Viwer HTML file: "
- + file);
+ System.out
+ .println("Creating BioJS MSA Viwer HTML file: " + file);
continue;
}
else if (outputFormat.equalsIgnoreCase("imgMap"))
else if (outputFormat.equalsIgnoreCase("eps"))
{
File outputFile = new File(file);
- System.out.println("Creating EPS file: "
- + outputFile.getAbsolutePath());
+ System.out.println(
+ "Creating EPS file: " + outputFile.getAbsolutePath());
af.createEPS(outputFile);
continue;
}
if (!headless && file == null && vamsasImport == null
&& jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
{
- file = jalview.bin.Cache.getDefault(
- "STARTUP_FILE",
+ file = jalview.bin.Cache.getDefault("STARTUP_FILE",
jalview.bin.Cache.getDefault("www.jalview.org",
"http://www.jalview.org")
+ "/examples/exampleFile_2_7.jar");
- if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar"))
+ if (file.equals(
+ "http://www.jalview.org/examples/exampleFile_2_3.jar"))
{
// hardwire upgrade of the startup file
file.replace("_2_3.jar", "_2_7.jar");
}
else
{
- System.err
- .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
+ System.err.println(
+ "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
+ groovyscript);
}
}
private static void showUsage()
{
- System.out
- .println("Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
+ System.out.println(
+ "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
+ "-nodisplay\tRun Jalview without User Interface.\n"
+ "-props FILE\tUse the given Jalview properties file instead of users default.\n"
+ "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
+ "-nousagestats\tTurn off google analytics tracking for this session.\n"
+ "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
// +
- // "-setprop PROPERTY=VALUE\tSet the given Jalview property, after all other properties files have been read\n\t (quote the 'PROPERTY=VALUE' pair to ensure spaces are passed in correctly)"
+ // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
+ // after all other properties files have been read\n\t
+ // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
+ // passed in correctly)"
+ "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
+ "-dasserver nickname=URL\tAdd and enable a das server with given nickname\n\t\t\t(alphanumeric or underscores only) for retrieval of features for all alignments.\n"
+ "\t\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n"
+ "\t\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n"
+ "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
// +
- // "-vdoc vamsas-document\tImport vamsas document into new session or join existing session with same URN\n"
+ // "-vdoc vamsas-document\tImport vamsas document into new
+ // session or join existing session with same URN\n"
// + "-vses vamsas-session\tJoin session with given URN\n"
+ "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n"
+ "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
/**
* start a User Config prompt asking if we can log usage statistics.
*/
- PromptUserConfig prompter = new PromptUserConfig(
- Desktop.desktop,
- "USAGESTATS",
- "Jalview Usage Statistics",
+ PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
+ "USAGESTATS", "Jalview Usage Statistics",
"Do you want to help make Jalview better by enabling "
+ "the collection of usage statistics with Google Analytics ?"
+ "\n\n(you can enable or disable usage tracking in the preferences)",
@Override
public void run()
{
- Cache.log
- .debug("Initialising googletracker for usage stats.");
+ Cache.log.debug(
+ "Initialising googletracker for usage stats.");
Cache.initGoogleTracker();
Cache.log.debug("Tracking enabled.");
}
try
{
tfile = File.createTempFile("jalview", "groovy");
- PrintWriter outfile = new PrintWriter(new OutputStreamWriter(
- new FileOutputStream(tfile)));
- BufferedReader br = new BufferedReader(new InputStreamReader(
- System.in));
+ PrintWriter outfile = new PrintWriter(
+ new OutputStreamWriter(new FileOutputStream(tfile)));
+ BufferedReader br = new BufferedReader(
+ new InputStreamReader(System.in));
String line = null;
while ((line = br.readLine()) != null)
{
} catch (Exception ex)
{
System.err.println("Failed to read from STDIN into tempfile "
- + ((tfile == null) ? "(tempfile wasn't created)" : tfile
- .toString()));
+ + ((tfile == null) ? "(tempfile wasn't created)"
+ : tfile.toString()));
ex.printStackTrace();
return;
}
sfile = tfile.toURI().toURL();
} catch (Exception x)
{
- System.err
- .println("Unexpected Malformed URL Exception for temporary file created from STDIN: "
+ System.err.println(
+ "Unexpected Malformed URL Exception for temporary file created from STDIN: "
+ tfile.toURI());
x.printStackTrace();
return;
nickname = data.substring(0, pos);
}
url = data.substring(pos + 1);
- if (url != null
- && (url.startsWith("http:") || url
- .startsWith("sequence:http:")))
+ if (url != null && (url.startsWith("http:")
+ || url.startsWith("sequence:http:")))
{
if (nickname == null)
{
locsources += "\t";
}
locsources = locsources + nickname + "|" + url;
- System.err
- .println("NOTE! dasserver parameter not yet really supported (got args of "
+ System.err.println(
+ "NOTE! dasserver parameter not yet really supported (got args of "
+ nickname + "|" + url);
if (source == null)
{
}
source.addElement(nickname);
}
- System.out.println("CMD [-dasserver " + data
- + "] executed successfully!");
+ System.out.println(
+ "CMD [-dasserver " + data + "] executed successfully!");
} // loop until no more server entries are found.
if (locsources != null && locsources.indexOf('|') > -1)
{
* @author $author$
* @version $Revision: 1.92 $
*/
-public class JalviewLite extends Applet implements
- StructureSelectionManagerProvider, JalviewLiteJsApi
+public class JalviewLite extends Applet
+ implements StructureSelectionManagerProvider, JalviewLiteJsApi
{
private static final String TRUE = "true";
final StructureSelectionManagerProvider me = this;
final int pos = apos;
// use vamsas listener to broadcast to all listeners in scope
- if (alignedPosition != null
- && (alignedPosition.trim().length() == 0 || alignedPosition
- .toLowerCase().indexOf("false") > -1))
+ if (alignedPosition != null && (alignedPosition.trim().length() == 0
+ || alignedPosition.toLowerCase().indexOf("false") > -1))
{
java.awt.EventQueue.invokeLater(new Runnable()
{
from--;
} catch (NumberFormatException ex)
{
- System.err
- .println("ERROR: Couldn't parse first integer in range element column selection string '"
+ System.err.println(
+ "ERROR: Couldn't parse first integer in range element column selection string '"
+ cl + "' - format is 'from-to'");
return;
}
to--;
} catch (NumberFormatException ex)
{
- System.err
- .println("ERROR: Couldn't parse second integer in range element column selection string '"
+ System.err.println(
+ "ERROR: Couldn't parse second integer in range element column selection string '"
+ cl + "' - format is 'from-to'");
return;
}
}
else
{
- System.err
- .println("ERROR: Couldn't parse integer from point selection element of column selection string '"
+ System.err.println(
+ "ERROR: Couldn't parse integer from point selection element of column selection string '"
+ cl + "'");
return;
}
@Override
public void run()
{
- alf.select(sel, csel, alf.getAlignViewport().getAlignment()
- .getHiddenColumns());
+ alf.select(sel, csel,
+ alf.getAlignViewport().getAlignment().getHiddenColumns());
}
});
}
* String, java.lang.String)
*/
@Override
- public String getSelectedSequencesAsAlignment(String format, String suffix)
+ public String getSelectedSequencesAsAlignment(String format,
+ String suffix)
{
return getSelectedSequencesAsAlignmentFrom(getDefaultTargetFrame(),
format, suffix);
listener = listener.trim();
if (listener.length() == 0)
{
- System.err
- .println("jalview Javascript error: Ignoring empty function for mouseover listener.");
+ System.err.println(
+ "jalview Javascript error: Ignoring empty function for mouseover listener.");
return;
}
}
if (debug)
{
System.err.println("Added a mouseover listener for "
- + ((af == null) ? "All frames" : "Just views for "
- + af.getAlignViewport().getSequenceSetId()));
+ + ((af == null) ? "All frames"
+ : "Just views for "
+ + af.getAlignViewport().getSequenceSetId()));
System.err.println("There are now " + javascriptListeners.size()
+ " listeners in total.");
}
listener = listener.trim();
if (listener.length() == 0)
{
- System.err
- .println("jalview Javascript error: Ignoring empty function for selection listener.");
+ System.err.println(
+ "jalview Javascript error: Ignoring empty function for selection listener.");
return;
}
}
if (debug)
{
System.err.println("Added a selection listener for "
- + ((af == null) ? "All frames" : "Just views for "
- + af.getAlignViewport().getSequenceSetId()));
+ + ((af == null) ? "All frames"
+ : "Just views for "
+ + af.getAlignViewport().getSequenceSetId()));
System.err.println("There are now " + javascriptListeners.size()
+ " listeners in total.");
}
listener = listener.trim();
if (listener.length() == 0)
{
- System.err
- .println("jalview Javascript error: Ignoring empty function for selection listener.");
+ System.err.println(
+ "jalview Javascript error: Ignoring empty function for selection listener.");
return;
}
}
{
Object lstn = javascriptListeners.elementAt(ms);
JsCallBack lstner = (JsCallBack) lstn;
- if ((af == null || lstner.getAlignFrame() == af)
- && (listener == null || lstner.getListenerFunction().equals(
- listener)))
+ if ((af == null || lstner.getAlignFrame() == af) && (listener == null
+ || lstner.getListenerFunction().equals(listener)))
{
javascriptListeners.removeElement(lstner);
msSize--;
* java.lang.String, java.lang.String)
*/
@Override
- public void mouseOverStructure(final String pdbResNum,
- final String chain, final String pdbfile)
+ public void mouseOverStructure(final String pdbResNum, final String chain,
+ final String pdbfile)
{
final StructureSelectionManagerProvider me = this;
java.awt.EventQueue.invokeLater(new Runnable()
chain, pdbfile);
if (debug)
{
- System.err.println("mouseOver for '" + pdbResNum
- + "' in chain '" + chain + "' in structure '" + pdbfile
- + "'");
+ System.err
+ .println("mouseOver for '" + pdbResNum + "' in chain '"
+ + chain + "' in structure '" + pdbfile + "'");
}
} catch (NumberFormatException e)
{
{
try
{
- alf.scrollTo(new Integer(topRow).intValue(), new Integer(
- leftHandColumn).intValue());
+ alf.scrollTo(new Integer(topRow).intValue(),
+ new Integer(leftHandColumn).intValue());
} catch (Exception ex)
{
} catch (Exception ex)
{
- System.err
- .println("Couldn't parse integer arguments (leftHandColumn='"
+ System.err.println(
+ "Couldn't parse integer arguments (leftHandColumn='"
+ leftHandColumn + "')");
ex.printStackTrace();
}
{
try
{
- BufferedReader reader = new BufferedReader(new InputStreamReader(
- url.openStream()));
+ BufferedReader reader = new BufferedReader(
+ new InputStreamReader(url.openStream()));
String line;
while ((line = reader.readLine()) != null)
{
} catch (Exception ex)
{
- System.err
- .println("Warning: No JalviewLite javascript callbacks available.");
+ System.err.println(
+ "Warning: No JalviewLite javascript callbacks available.");
if (debug)
{
ex.printStackTrace();
}
else
{
- throw new Error(
- MessageManager
- .getString("error.invalid_separator_parameter"));
+ throw new Error(MessageManager
+ .getString("error.invalid_separator_parameter"));
}
}
int r = 255;
{
// do onInit with the JS executor thread
new JSFunctionExec(this).executeJavascriptFunction(true,
- initjscallback, null, "Calling oninit callback '"
- + initjscallback + "'.");
+ initjscallback, null,
+ "Calling oninit callback '" + initjscallback + "'.");
} catch (Exception e)
{
System.err.println("Exception when executing _oninit callback '"
g.fillRect(0, 0, getSize().width, getSize().height);
g.setColor(Color.red);
g.drawString(
- MessageManager.getString("label.jalview_cannot_open_file"),
- 5, 15);
+ MessageManager.getString("label.jalview_cannot_open_file"), 5,
+ 15);
g.drawString("\"" + file + "\"", 5, 30);
}
else if (embedded)
}
if (!jmolAvailable)
{
- System.out
- .println("Jmol not available - Using MCview for structures");
+ System.out.println(
+ "Jmol not available - Using MCview for structures");
}
} catch (java.lang.ClassNotFoundException ex)
{
jmolAvailable = false;
if (debug)
{
- System.err
- .println("Skipping Jmol check. Will use MCView (probably)");
+ System.err.println(
+ "Skipping Jmol check. Will use MCView (probably)");
}
}
checkedForJmol = true;
*/
private void startLoading()
{
- dbgMsg("Loading thread started with:\n>>file\n" + _file + ">>endfile");
+ dbgMsg("Loading thread started with:\n>>file\n" + _file
+ + ">>endfile");
dbgMsg("Loading started.");
if (protocol == DataSourceType.PASTE)
{
- newAlignFrame.setTitle(MessageManager.formatMessage(
- "label.sequences_from", new Object[] { applet
- .getDocumentBase().toString() }));
+ newAlignFrame.setTitle(MessageManager
+ .formatMessage("label.sequences_from", new Object[]
+ { applet.getDocumentBase().toString() }));
}
newAlignFrame.statusBar.setText(MessageManager.formatMessage(
- "label.successfully_loaded_file",
- new Object[] { resolvedFile }));
+ "label.successfully_loaded_file", new Object[]
+ { resolvedFile }));
return newAlignFrame;
}
dbgMsg(">>>Dump finished.");
} catch (Exception e)
{
- System.err
- .println("Exception when trying to dump the content of the file parameter.");
+ System.err.println(
+ "Exception when trying to dump the content of the file parameter.");
e.printStackTrace();
}
}
* related to JAL-434
*/
- applet.setAlignPdbStructures(getDefaultParameter("alignpdbfiles",
- false));
+ applet.setAlignPdbStructures(
+ getDefaultParameter("alignpdbfiles", false));
/*
* <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B
* PDB|1GAQ|1GAQ|C">
Vector pdbs = new Vector();
// create a lazy matcher if we're asked to
jalview.analysis.SequenceIdMatcher matcher = (applet
- .getDefaultParameter("relaxedidmatch", false)) ? new jalview.analysis.SequenceIdMatcher(
- alignFrame.getAlignViewport().getAlignment()
- .getSequencesArray()) : null;
+ .getDefaultParameter("relaxedidmatch", false))
+ ? new jalview.analysis.SequenceIdMatcher(
+ alignFrame.getAlignViewport().getAlignment()
+ .getSequencesArray())
+ : null;
String param;
do
String sequence = applet.getParameter("PDBSEQ");
if (sequence != null)
{
- seqs = new SequenceI[] { matcher == null ? (Sequence) alignFrame
- .getAlignViewport().getAlignment().findName(sequence)
+ seqs = new SequenceI[] { matcher == null
+ ? (Sequence) alignFrame.getAlignViewport()
+ .getAlignment().findName(sequence)
: matcher.findIdMatch(sequence) };
}
tmp2.add(st2.nextToken());
seqstring = st2.nextToken();
}
- tmp.add(matcher == null ? (Sequence) alignFrame
- .getAlignViewport().getAlignment()
- .findName(seqstring) : matcher.findIdMatch(seqstring));
+ tmp.add(matcher == null
+ ? (Sequence) alignFrame.getAlignViewport()
+ .getAlignment().findName(seqstring)
+ : matcher.findIdMatch(seqstring));
}
seqs = tmp.toArray(new SequenceI[tmp.size()]);
if (seqs[i] != null)
{
((Sequence) seqs[i]).addPDBId(pdb);
- StructureSelectionManager.getStructureSelectionManager(
- applet).registerPDBEntry(pdb);
+ StructureSelectionManager
+ .getStructureSelectionManager(applet)
+ .registerPDBEntry(pdb);
}
else
{
{
// this may not really be a problem but we give a warning
// anyway
- System.err
- .println("Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "
+ System.err.println(
+ "Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "
+ i + ")");
}
}
PDBEntry[] pdb = new PDBEntry[pdbs.size()];
String[][] chains = new String[pdbs.size()][];
String[] protocols = new String[pdbs.size()];
- for (int pdbsi = 0, pdbsiSize = pdbs.size(); pdbsi < pdbsiSize; pdbsi++)
+ for (int pdbsi = 0, pdbsiSize = pdbs
+ .size(); pdbsi < pdbsiSize; pdbsi++)
{
Object[] o = (Object[]) pdbs.elementAt(pdbsi);
pdb[pdbsi] = (PDBEntry) o[0];
}
else
{
- System.err
- .println("Annotations were not added from annotation file '"
+ System.err.println(
+ "Annotations were not added from annotation file '"
+ param + "'");
}
}
{
if (debug)
{
- System.err
- .println("Attempting to load T-COFFEE score file from the scoreFile parameter");
+ System.err.println(
+ "Attempting to load T-COFFEE score file from the scoreFile parameter");
}
result = alignFrame.loadScoreFile(sScoreFile);
if (!result)
{
- System.err
- .println("Failed to parse T-COFFEE parameter as a valid score file ('"
+ System.err.println(
+ "Failed to parse T-COFFEE parameter as a valid score file ('"
+ sScoreFile + "')");
}
} catch (Exception e)
{
return initialAlignFrame;
}
- System.err
- .println("Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");
+ System.err.println(
+ "Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");
return null;
}
}
if (debug)
{
- System.err.println("Empty Array from '" + separator
- + "' separated List");
+ System.err.println(
+ "Empty Array from '" + separator + "' separated List");
}
return null;
}
}
if (debug)
{
- System.err.println("Returning '" + separator
- + "' separated List:\n");
+ System.err
+ .println("Returning '" + separator + "' separated List:\n");
System.err.println(v);
}
return v.toString();
}
if (debug)
{
- System.err.println("Returning empty '" + separator
- + "' separated List\n");
+ System.err.println(
+ "Returning empty '" + separator + "' separated List\n");
}
return "" + separator;
}
@Override
public String getFeatureGroups()
{
- String lst = arrayToSeparatorList(getDefaultTargetFrame()
- .getFeatureGroups());
+ String lst = arrayToSeparatorList(
+ getDefaultTargetFrame().getFeatureGroups());
return lst;
}
@Override
public String getFeatureGroupsOfState(boolean visible)
{
- return arrayToSeparatorList(getDefaultTargetFrame()
- .getFeatureGroupsOfState(visible));
+ return arrayToSeparatorList(
+ getDefaultTargetFrame().getFeatureGroupsOfState(visible));
}
/*
Color col = ColorUtils.parseColourString(colprop);
if (col == null)
{
- System.err.println("Couldn't parse '" + colprop
- + "' as a colour for " + colparam);
+ System.err.println("Couldn't parse '" + colprop + "' as a colour for "
+ + colparam);
}
return (col == null) ? defcolour : col;
}
String codebase = localref.toString();
String localfile = localref.getFile();
resolvedPath = codebase.substring(0,
- codebase.length() - localfile.length())
- + targetPath;
+ codebase.length() - localfile.length()) + targetPath;
return resolvedPath;
}
}
if (debug)
{
- System.err.println("resolveUrlForLocalOrAbsolute returning "
- + resolvedPath);
+ System.err.println(
+ "resolveUrlForLocalOrAbsolute returning " + resolvedPath);
}
return resolvedPath;
}
// form valid URL
// Should really use docbase, not codebase.
URL prepend;
- url = resolveUrlForLocalOrAbsolute(
- url,
- prepend = getDefaultParameter("resolvetocodebase", false) ? getCodeBase()
+ url = resolveUrlForLocalOrAbsolute(url,
+ prepend = getDefaultParameter("resolvetocodebase", false)
+ ? getCodeBase()
: getDocumentBase());
if (debug)
{
- System.err
- .println("Show url (prepended "
- + prepend
- + " - toggle resolvetocodebase if code/docbase resolution is wrong): "
- + url);
+ System.err.println("Show url (prepended " + prepend
+ + " - toggle resolvetocodebase if code/docbase resolution is wrong): "
+ + url);
}
}
else
} catch (Exception ex)
{
- System.out.println("Exception checking resources: " + file + " "
- + ex);
+ System.out.println(
+ "Exception checking resources: " + file + " " + ex);
}
if (file.indexOf("://") > -1)
{
+ " cannot be read with protocol==" + protocol);
return;
}
- FileFormatI format = FileFormats.getInstance().forName(
- getParameter("format"));
+ FileFormatI format = FileFormats.getInstance()
+ .forName(getParameter("format"));
if (format == null)
{
format = new IdentifyFile().identify(file, protocol);
}
if (al != null)
{
- System.out.println(new AppletFormatAdapter().formatSequences(
- FileFormat.Fasta, al, false));
+ System.out.println(new AppletFormatAdapter()
+ .formatSequences(FileFormat.Fasta, al, false));
}
} catch (Exception e)
{
throws org.exolab.castor.xml.MarshalException,
org.exolab.castor.xml.ValidationException
{
- return (jalview.binding.Alignment) Unmarshaller.unmarshal(
- jalview.binding.Alignment.class, reader);
+ return (jalview.binding.Alignment) Unmarshaller
+ .unmarshal(jalview.binding.Alignment.class, reader);
}
/**
throws org.exolab.castor.xml.MarshalException,
org.exolab.castor.xml.ValidationException
{
- return (jalview.binding.Annotation) Unmarshaller.unmarshal(
- jalview.binding.Annotation.class, reader);
+ return (jalview.binding.Annotation) Unmarshaller
+ .unmarshal(jalview.binding.Annotation.class, reader);
}
/**
throws org.exolab.castor.xml.MarshalException,
org.exolab.castor.xml.ValidationException
{
- return (jalview.binding.AnnotationElement) Unmarshaller.unmarshal(
- jalview.binding.AnnotationElement.class, reader);
+ return (jalview.binding.AnnotationElement) Unmarshaller
+ .unmarshal(jalview.binding.AnnotationElement.class, reader);
}
/**
* if this object is an invalid instance according to the schema
* @return the unmarshaled jalview.binding.Colour
*/
- public static jalview.binding.Colour unmarshal(final java.io.Reader reader)
+ public static jalview.binding.Colour unmarshal(
+ final java.io.Reader reader)
throws org.exolab.castor.xml.MarshalException,
org.exolab.castor.xml.ValidationException
{
- return (jalview.binding.Colour) Unmarshaller.unmarshal(
- jalview.binding.Colour.class, reader);
+ return (jalview.binding.Colour) Unmarshaller
+ .unmarshal(jalview.binding.Colour.class, reader);
}
/**
throws org.exolab.castor.xml.MarshalException,
org.exolab.castor.xml.ValidationException
{
- return (jalview.binding.Feature) Unmarshaller.unmarshal(
- jalview.binding.Feature.class, reader);
+ return (jalview.binding.Feature) Unmarshaller
+ .unmarshal(jalview.binding.Feature.class, reader);
}
/**
// check bounds for index
if (index < 0 || index >= this._settingList.size())
{
- throw new IndexOutOfBoundsException("getSetting: Index value '"
- + index + "' not in range [0.."
- + (this._settingList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(
+ "getSetting: Index value '" + index + "' not in range [0.."
+ + (this._settingList.size() - 1) + "]");
}
return (jalview.binding.Setting) _settingList.get(index);
// check bounds for index
if (index < 0 || index >= this._settingList.size())
{
- throw new IndexOutOfBoundsException("setSetting: Index value '"
- + index + "' not in range [0.."
- + (this._settingList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(
+ "setSetting: Index value '" + index + "' not in range [0.."
+ + (this._settingList.size() - 1) + "]");
}
this._settingList.set(index, vSetting);
throws org.exolab.castor.xml.MarshalException,
org.exolab.castor.xml.ValidationException
{
- return (jalview.binding.FeatureSettings) Unmarshaller.unmarshal(
- jalview.binding.FeatureSettings.class, reader);
+ return (jalview.binding.FeatureSettings) Unmarshaller
+ .unmarshal(jalview.binding.FeatureSettings.class, reader);
}
/**
throws org.exolab.castor.xml.MarshalException,
org.exolab.castor.xml.ValidationException
{
- return (jalview.binding.Feature) Unmarshaller.unmarshal(
- jalview.binding.Features.class, reader);
+ return (jalview.binding.Feature) Unmarshaller
+ .unmarshal(jalview.binding.Features.class, reader);
}
/**
* if this object is an invalid instance according to the schema
* @return the unmarshaled jalview.binding.JGroup
*/
- public static jalview.binding.JGroup unmarshal(final java.io.Reader reader)
+ public static jalview.binding.JGroup unmarshal(
+ final java.io.Reader reader)
throws org.exolab.castor.xml.MarshalException,
org.exolab.castor.xml.ValidationException
{
- return (jalview.binding.JGroup) Unmarshaller.unmarshal(
- jalview.binding.JGroup.class, reader);
+ return (jalview.binding.JGroup) Unmarshaller
+ .unmarshal(jalview.binding.JGroup.class, reader);
}
/**
// check bounds for index
if (index < 0 || index >= this._featuresList.size())
{
- throw new IndexOutOfBoundsException("getFeatures: Index value '"
- + index + "' not in range [0.."
- + (this._featuresList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(
+ "getFeatures: Index value '" + index + "' not in range [0.."
+ + (this._featuresList.size() - 1) + "]");
}
return (jalview.binding.Features) _featuresList.get(index);
// check bounds for index
if (index < 0 || index >= this._pdbidsList.size())
{
- throw new IndexOutOfBoundsException("getPdbids: Index value '"
- + index + "' not in range [0.."
- + (this._pdbidsList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(
+ "getPdbids: Index value '" + index + "' not in range [0.."
+ + (this._pdbidsList.size() - 1) + "]");
}
return (jalview.binding.Pdbids) _pdbidsList.get(index);
// check bounds for index
if (index < 0 || index >= this._featuresList.size())
{
- throw new IndexOutOfBoundsException("setFeatures: Index value '"
- + index + "' not in range [0.."
- + (this._featuresList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(
+ "setFeatures: Index value '" + index + "' not in range [0.."
+ + (this._featuresList.size() - 1) + "]");
}
this._featuresList.set(index, vFeatures);
// check bounds for index
if (index < 0 || index >= this._pdbidsList.size())
{
- throw new IndexOutOfBoundsException("setPdbids: Index value '"
- + index + "' not in range [0.."
- + (this._pdbidsList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(
+ "setPdbids: Index value '" + index + "' not in range [0.."
+ + (this._pdbidsList.size() - 1) + "]");
}
this._pdbidsList.set(index, vPdbids);
throws org.exolab.castor.xml.MarshalException,
org.exolab.castor.xml.ValidationException
{
- return (jalview.binding.JSeq) Unmarshaller.unmarshal(
- jalview.binding.JSeq.class, reader);
+ return (jalview.binding.JSeq) Unmarshaller
+ .unmarshal(jalview.binding.JSeq.class, reader);
}
/**
throws org.exolab.castor.xml.MarshalException,
org.exolab.castor.xml.ValidationException
{
- return (jalview.binding.JalviewModel) Unmarshaller.unmarshal(
- jalview.binding.JalviewModel.class, reader);
+ return (jalview.binding.JalviewModel) Unmarshaller
+ .unmarshal(jalview.binding.JalviewModel.class, reader);
}
/**
// check bounds for index
if (index < 0 || index >= this._JGroupList.size())
{
- throw new IndexOutOfBoundsException("getJGroup: Index value '"
- + index + "' not in range [0.."
- + (this._JGroupList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(
+ "getJGroup: Index value '" + index + "' not in range [0.."
+ + (this._JGroupList.size() - 1) + "]");
}
return (jalview.binding.JGroup) _JGroupList.get(index);
// check bounds for index
if (index < 0 || index >= this._viewportList.size())
{
- throw new IndexOutOfBoundsException("getViewport: Index value '"
- + index + "' not in range [0.."
- + (this._viewportList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(
+ "getViewport: Index value '" + index + "' not in range [0.."
+ + (this._viewportList.size() - 1) + "]");
}
return (jalview.binding.Viewport) _viewportList.get(index);
// check bounds for index
if (index < 0 || index >= this._JGroupList.size())
{
- throw new IndexOutOfBoundsException("setJGroup: Index value '"
- + index + "' not in range [0.."
- + (this._JGroupList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(
+ "setJGroup: Index value '" + index + "' not in range [0.."
+ + (this._JGroupList.size() - 1) + "]");
}
this._JGroupList.set(index, vJGroup);
// check bounds for index
if (index < 0 || index >= this._viewportList.size())
{
- throw new IndexOutOfBoundsException("setViewport: Index value '"
- + index + "' not in range [0.."
- + (this._viewportList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(
+ "setViewport: Index value '" + index + "' not in range [0.."
+ + (this._viewportList.size() - 1) + "]");
}
this._viewportList.set(index, vViewport);
throws org.exolab.castor.xml.MarshalException,
org.exolab.castor.xml.ValidationException
{
- return (jalview.binding.JalviewModelSequence) Unmarshaller.unmarshal(
- jalview.binding.JalviewModelSequence.class, reader);
+ return (jalview.binding.JalviewModelSequence) Unmarshaller
+ .unmarshal(jalview.binding.JalviewModelSequence.class, reader);
}
/**
// check bounds for index
if (index < 0 || index >= this._colourList.size())
{
- throw new IndexOutOfBoundsException("getColour: Index value '"
- + index + "' not in range [0.."
- + (this._colourList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(
+ "getColour: Index value '" + index + "' not in range [0.."
+ + (this._colourList.size() - 1) + "]");
}
return (Colour) _colourList.get(index);
// check bounds for index
if (index < 0 || index >= this._colourList.size())
{
- throw new IndexOutOfBoundsException("setColour: Index value '"
- + index + "' not in range [0.."
- + (this._colourList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(
+ "setColour: Index value '" + index + "' not in range [0.."
+ + (this._colourList.size() - 1) + "]");
}
this._colourList.set(index, vColour);
throws org.exolab.castor.xml.MarshalException,
org.exolab.castor.xml.ValidationException
{
- return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(
- jalview.binding.JalviewUserColours.class, reader);
+ return (jalview.binding.JalviewUserColours) Unmarshaller
+ .unmarshal(jalview.binding.JalviewUserColours.class, reader);
}
/**
throws org.exolab.castor.xml.MarshalException,
org.exolab.castor.xml.ValidationException
{
- return (jalview.binding.Pdbentry) Unmarshaller.unmarshal(
- jalview.binding.Pdbentry.class, reader);
+ return (jalview.binding.Pdbentry) Unmarshaller
+ .unmarshal(jalview.binding.Pdbentry.class, reader);
}
/**
// check bounds for index
if (index < 0 || index >= this._propertyList.size())
{
- throw new IndexOutOfBoundsException("getProperty: Index value '"
- + index + "' not in range [0.."
- + (this._propertyList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(
+ "getProperty: Index value '" + index + "' not in range [0.."
+ + (this._propertyList.size() - 1) + "]");
}
return (jalview.binding.Property) _propertyList.get(index);
// check bounds for index
if (index < 0 || index >= this._propertyList.size())
{
- throw new IndexOutOfBoundsException("setProperty: Index value '"
- + index + "' not in range [0.."
- + (this._propertyList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(
+ "setProperty: Index value '" + index + "' not in range [0.."
+ + (this._propertyList.size() - 1) + "]");
}
this._propertyList.set(index, vProperty);
throws org.exolab.castor.xml.MarshalException,
org.exolab.castor.xml.ValidationException
{
- return (jalview.binding.Pdbentry) Unmarshaller.unmarshal(
- jalview.binding.Pdbids.class, reader);
+ return (jalview.binding.Pdbentry) Unmarshaller
+ .unmarshal(jalview.binding.Pdbids.class, reader);
}
/**
throws org.exolab.castor.xml.MarshalException,
org.exolab.castor.xml.ValidationException
{
- return (jalview.binding.Property) Unmarshaller.unmarshal(
- jalview.binding.Property.class, reader);
+ return (jalview.binding.Property) Unmarshaller
+ .unmarshal(jalview.binding.Property.class, reader);
}
/**
throws org.exolab.castor.xml.MarshalException,
org.exolab.castor.xml.ValidationException
{
- return (jalview.binding.SequenceType) Unmarshaller.unmarshal(
- jalview.binding.Sequence.class, reader);
+ return (jalview.binding.SequenceType) Unmarshaller
+ .unmarshal(jalview.binding.Sequence.class, reader);
}
/**
// check bounds for index
if (index < 0 || index >= this._annotationList.size())
{
- throw new IndexOutOfBoundsException("getAnnotation: Index value '"
- + index + "' not in range [0.."
- + (this._annotationList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(
+ "getAnnotation: Index value '" + index + "' not in range [0.."
+ + (this._annotationList.size() - 1) + "]");
}
return (jalview.binding.Annotation) _annotationList.get(index);
// check bounds for index
if (index < 0 || index >= this._sequenceList.size())
{
- throw new IndexOutOfBoundsException("getSequence: Index value '"
- + index + "' not in range [0.."
- + (this._sequenceList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(
+ "getSequence: Index value '" + index + "' not in range [0.."
+ + (this._sequenceList.size() - 1) + "]");
}
return (jalview.binding.Sequence) _sequenceList.get(index);
// check bounds for index
if (index < 0 || index >= this._annotationList.size())
{
- throw new IndexOutOfBoundsException("setAnnotation: Index value '"
- + index + "' not in range [0.."
- + (this._annotationList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(
+ "setAnnotation: Index value '" + index + "' not in range [0.."
+ + (this._annotationList.size() - 1) + "]");
}
this._annotationList.set(index, vAnnotation);
// check bounds for index
if (index < 0 || index >= this._sequenceList.size())
{
- throw new IndexOutOfBoundsException("setSequence: Index value '"
- + index + "' not in range [0.."
- + (this._sequenceList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(
+ "setSequence: Index value '" + index + "' not in range [0.."
+ + (this._sequenceList.size() - 1) + "]");
}
this._sequenceList.set(index, vSequence);
throws org.exolab.castor.xml.MarshalException,
org.exolab.castor.xml.ValidationException
{
- return (jalview.binding.SequenceSet) Unmarshaller.unmarshal(
- jalview.binding.SequenceSet.class, reader);
+ return (jalview.binding.SequenceSet) Unmarshaller
+ .unmarshal(jalview.binding.SequenceSet.class, reader);
}
/**
throws org.exolab.castor.xml.MarshalException,
org.exolab.castor.xml.ValidationException
{
- return (jalview.binding.SequenceType) Unmarshaller.unmarshal(
- jalview.binding.SequenceType.class, reader);
+ return (jalview.binding.SequenceType) Unmarshaller
+ .unmarshal(jalview.binding.SequenceType.class, reader);
}
/**
throws org.exolab.castor.xml.MarshalException,
org.exolab.castor.xml.ValidationException
{
- return (jalview.binding.Setting) Unmarshaller.unmarshal(
- jalview.binding.Setting.class, reader);
+ return (jalview.binding.Setting) Unmarshaller
+ .unmarshal(jalview.binding.Setting.class, reader);
}
/**
throws org.exolab.castor.xml.MarshalException,
org.exolab.castor.xml.ValidationException
{
- return (jalview.binding.Tree) Unmarshaller.unmarshal(
- jalview.binding.Tree.class, reader);
+ return (jalview.binding.Tree) Unmarshaller
+ .unmarshal(jalview.binding.Tree.class, reader);
}
/**
*
* @version $Revision$ $Date$
*/
-public class UserColourScheme extends JalviewUserColours implements
- java.io.Serializable
+public class UserColourScheme extends JalviewUserColours
+ implements java.io.Serializable
{
// ----------------/
throws org.exolab.castor.xml.MarshalException,
org.exolab.castor.xml.ValidationException
{
- return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(
- jalview.binding.UserColourScheme.class, reader);
+ return (jalview.binding.JalviewUserColours) Unmarshaller
+ .unmarshal(jalview.binding.UserColourScheme.class, reader);
}
/**
throws org.exolab.castor.xml.MarshalException,
org.exolab.castor.xml.ValidationException
{
- return (jalview.binding.UserColours) Unmarshaller.unmarshal(
- jalview.binding.UserColours.class, reader);
+ return (jalview.binding.UserColours) Unmarshaller
+ .unmarshal(jalview.binding.UserColours.class, reader);
}
/**
* @throws java.lang.IndexOutOfBoundsException
* if the index given is outside the bounds of the collection
*/
- public void addSequenceSet(final int index, final SequenceSet vSequenceSet)
+ public void addSequenceSet(final int index,
+ final SequenceSet vSequenceSet)
throws java.lang.IndexOutOfBoundsException
{
this._sequenceSetList.add(index, vSequenceSet);
// check bounds for index
if (index < 0 || index >= this._alignmentList.size())
{
- throw new IndexOutOfBoundsException("getAlignment: Index value '"
- + index + "' not in range [0.."
- + (this._alignmentList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(
+ "getAlignment: Index value '" + index + "' not in range [0.."
+ + (this._alignmentList.size() - 1) + "]");
}
return (Alignment) _alignmentList.get(index);
// check bounds for index
if (index < 0 || index >= this._alignmentList.size())
{
- throw new IndexOutOfBoundsException("setAlignment: Index value '"
- + index + "' not in range [0.."
- + (this._alignmentList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(
+ "setAlignment: Index value '" + index + "' not in range [0.."
+ + (this._alignmentList.size() - 1) + "]");
}
this._alignmentList.set(index, vAlignment);
* @throws java.lang.IndexOutOfBoundsException
* if the index given is outside the bounds of the collection
*/
- public void setSequenceSet(final int index, final SequenceSet vSequenceSet)
+ public void setSequenceSet(final int index,
+ final SequenceSet vSequenceSet)
throws java.lang.IndexOutOfBoundsException
{
// check bounds for index
* if this object is an invalid instance according to the schema
* @return the unmarshaled jalview.binding.VAMSAS
*/
- public static jalview.binding.VAMSAS unmarshal(final java.io.Reader reader)
+ public static jalview.binding.VAMSAS unmarshal(
+ final java.io.Reader reader)
throws org.exolab.castor.xml.MarshalException,
org.exolab.castor.xml.ValidationException
{
- return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(
- jalview.binding.VAMSAS.class, reader);
+ return (jalview.binding.VAMSAS) Unmarshaller
+ .unmarshal(jalview.binding.VAMSAS.class, reader);
}
/**
* if this object is an invalid instance according to the schema
* @return the unmarshaled jalview.binding.VAMSAS
*/
- public static jalview.binding.VAMSAS unmarshal(final java.io.Reader reader)
+ public static jalview.binding.VAMSAS unmarshal(
+ final java.io.Reader reader)
throws org.exolab.castor.xml.MarshalException,
org.exolab.castor.xml.ValidationException
{
- return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(
- jalview.binding.VamsasModel.class, reader);
+ return (jalview.binding.VAMSAS) Unmarshaller
+ .unmarshal(jalview.binding.VamsasModel.class, reader);
}
/**
throws org.exolab.castor.xml.MarshalException,
org.exolab.castor.xml.ValidationException
{
- return (jalview.binding.Viewport) Unmarshaller.unmarshal(
- jalview.binding.Viewport.class, reader);
+ return (jalview.binding.Viewport) Unmarshaller
+ .unmarshal(jalview.binding.Viewport.class, reader);
}
/**
/**
* Check a contiguous edit; either
* <ul>
- * <li>a new Insert <n> positions to the right of the last <insert n>, or</li>
+ * <li>a new Insert <n> positions to the right of the last <insert n>,
+ * or</li>
* <li>a new Delete <n> gaps which is <n> positions to the left of the last
* delete.</li>
* </ul>
*/
- boolean contiguous = (action == Action.INSERT_GAP && e.position == lastEdit.position
- + lastEdit.number)
- || (action == Action.DELETE_GAP && e.position + e.number == lastEdit.position);
+ boolean contiguous = (action == Action.INSERT_GAP
+ && e.position == lastEdit.position + lastEdit.number)
+ || (action == Action.DELETE_GAP
+ && e.position + e.number == lastEdit.position);
if (contiguous)
{
/*
{
command.seqs[s].insertCharAt(command.position, command.number,
command.gapChar);
- // System.out.println("pos: "+command.position+" number: "+command.number);
+ // System.out.println("pos: "+command.position+" number:
+ // "+command.number);
}
adjustAnnotations(command, true, false, null);
{
for (int s = 0; s < command.seqs.length; s++)
{
- command.seqs[s].deleteChars(command.position, command.position
- + command.number);
+ command.seqs[s].deleteChars(command.position,
+ command.position + command.number);
}
adjustAnnotations(command, false, false, null);
// we are redoing an undone cut.
sequence.setDatasetSequence(null);
}
- sequence.deleteChars(command.position, command.position
- + command.number);
+ sequence.deleteChars(command.position,
+ command.position + command.number);
if (command.oldds != null && command.oldds[i] != null)
{
// oldds entry contains the cut dataset sequence.
command.oldds = new SequenceI[command.seqs.length];
}
command.oldds[i] = oldds;
- adjustFeatures(
- command,
- i,
+ adjustFeatures(command, i,
sequence.findPosition(command.position),
- sequence.findPosition(command.position + command.number),
+ sequence.findPosition(
+ command.position + command.number),
false);
}
}
{
newDSNeeded = true;
start = command.seqs[i].findPosition(command.position);
- end = command.seqs[i].findPosition(command.position
- + command.number);
+ end = command.seqs[i]
+ .findPosition(command.position + command.number);
}
if (command.seqs[i].getStart() == start)
{
tmp = new StringBuffer(oldstring.substring(0, start));
tmp.append(command.string[i]);
String nogaprep = jalview.analysis.AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars, new String(
- command.string[i]));
+ jalview.util.Comparison.GapChars,
+ new String(command.string[i]));
int ipos = command.seqs[i].findPosition(start)
- command.seqs[i].getStart();
tmp.append(oldstring.substring(end));
command.seqs[i].setSequence(tmp.toString());
command.string[i] = oldstring.substring(start, end).toCharArray();
String nogapold = jalview.analysis.AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars, new String(
- command.string[i]));
+ jalview.util.Comparison.GapChars,
+ new String(command.string[i]));
if (!nogaprep.toLowerCase().equals(nogapold.toLowerCase()))
{
if (newDSWasNeeded)
tmp = saved;
command.deletedAnnotationRows.put(command.seqs[s], saved);
// and then remove any annotation in the other views
- for (int alview = 0; views != null && alview < views.length; alview++)
+ for (int alview = 0; views != null
+ && alview < views.length; alview++)
{
if (views[alview] != command.al)
{
}
// and then duplicate added annotation on every other alignment
// view
- for (int vnum = 0; views != null && vnum < views.length; vnum++)
+ for (int vnum = 0; views != null
+ && vnum < views.length; vnum++)
{
if (views[vnum] != command.al)
{
}
System.arraycopy(annotations[a].annotations, command.position,
- temp, command.position + command.number, aSize
- - command.position);
+ temp, command.position + command.number,
+ aSize - command.position);
}
else
{
annotations[a].annotations.length - command.position);
if (copylen > 0)
{
- System.arraycopy(annotations[a].annotations,
- command.position, deleted, 0, copylen); // command.number);
+ System.arraycopy(annotations[a].annotations, command.position,
+ deleted, 0, copylen); // command.number);
}
}
if (annotations[a].annotations.length > command.position
+ command.number)
{
- System.arraycopy(annotations[a].annotations, command.position
- + command.number, temp, command.position,
- annotations[a].annotations.length - command.position
- - command.number); // aSize
+ System.arraycopy(annotations[a].annotations,
+ command.position + command.number, temp,
+ command.position, annotations[a].annotations.length
+ - command.position - command.number); // aSize
}
}
else
if (!delete && startCol > -1)
{
- this.appendEdit(Action.DELETE_GAP, new SequenceI[] { seqs[s] },
- start + startCol - deletedCols, endCol - startCol, al,
- false, null);
+ this.appendEdit(
+ Action.DELETE_GAP, new SequenceI[]
+ { seqs[s] }, start + startCol - deletedCols,
+ endCol - startCol, al, false, null);
deletedCols += (endCol - startCol);
startCol = -1;
}
if (delete && startCol > -1)
{
- this.appendEdit(Action.DELETE_GAP, new SequenceI[] { seqs[s] },
- start + startCol - deletedCols, jSize - startCol, al,
- false, null);
+ this.appendEdit(
+ Action.DELETE_GAP, new SequenceI[]
+ { seqs[s] }, start + startCol - deletedCols,
+ jSize - startCol, al, false, null);
}
}
SequenceGroup[] gps = null;
if (sg != null && (cs == null || cs.isEmpty()))
{
- gps = jalview.analysis.Grouping.makeGroupsFrom(viewport
- .getSequenceSelection(), viewport.getAlignmentView(true)
- .getSequenceStrings(viewport.getGapCharacter()), viewport
- .getAlignment().getGroups());
+ gps = jalview.analysis.Grouping.makeGroupsFrom(
+ viewport.getSequenceSelection(),
+ viewport.getAlignmentView(true)
+ .getSequenceStrings(viewport.getGapCharacter()),
+ viewport.getAlignment().getGroups());
}
else
{
{
gps = jalview.analysis.Grouping.makeGroupsFromCols(
(sg == null) ? viewport.getAlignment().getSequencesArray()
- : sg.getSequences().toArray(new SequenceI[0]), cs,
- viewport.getAlignment().getGroups());
+ : sg.getSequences().toArray(new SequenceI[0]),
+ cs, viewport.getAlignment().getGroups());
}
}
if (gps != null)
// JBPNote this routine could also mark rows, not just columns.
// need a decent query structure to allow all types of feature searches
BitSet bs = new BitSet();
- SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null || extendCurrent) ? viewport
- .getAlignment() : viewport.getSelectionGroup();
+ SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null
+ || extendCurrent) ? viewport.getAlignment()
+ : viewport.getSelectionGroup();
int nseq = findColumnsWithFeature(featureType, sqcol, bs);
{
viewport.setColumnSelection(cs);
alignPanel.paintAlignment(true);
- int columnCount = invert ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
- - bs.cardinality()
+ int columnCount = invert
+ ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
+ - bs.cardinality()
: bs.cardinality();
avcg.setStatus(MessageManager.formatMessage(
- "label.view_controller_toggled_marked",
- new String[] {
- toggle ? MessageManager.getString("label.toggled")
- : MessageManager.getString("label.marked"),
+ "label.view_controller_toggled_marked", new String[]
+ { toggle ? MessageManager.getString("label.toggled")
+ : MessageManager.getString("label.marked"),
String.valueOf(columnCount),
invert ? MessageManager
.getString("label.not_containing")
}
else
{
- avcg.setStatus(MessageManager.formatMessage(
- "label.no_feature_of_type_found",
- new String[] { featureType }));
+ avcg.setStatus(MessageManager
+ .formatMessage("label.no_feature_of_type_found", new String[]
+ { featureType }));
if (!extendCurrent)
{
cs.clear();
}
SequenceI[] oldOrder = al.getSequencesArray();
AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method);
- avcg.addHistoryItem(new OrderCommand(methodText, oldOrder, viewport
- .getAlignment()));
+ avcg.addHistoryItem(new OrderCommand(methodText, oldOrder,
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
boolean featuresFile = false;
try
{
- featuresFile = new FeaturesFile(false, file, protocol).parse(viewport
- .getAlignment().getDataset(), alignPanel.getFeatureRenderer()
- .getFeatureColours(), false, relaxedIdMatching);
+ featuresFile = new FeaturesFile(false, file, protocol).parse(
+ viewport.getAlignment().getDataset(),
+ alignPanel.getFeatureRenderer().getFeatureColours(), false,
+ relaxedIdMatching);
} catch (Exception ex)
{
ex.printStackTrace();
}
// JBPNote this routine could also mark rows, not just columns.
BitSet bs = new BitSet();
- SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null || extendCurrent) ? viewport
- .getAlignment() : viewport.getSelectionGroup();
+ SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null
+ || extendCurrent) ? viewport.getAlignment()
+ : viewport.getSelectionGroup();
// this could be a lambda... - the remains of the method is boilerplate,
// except for the different messages for reporting selection.
{
viewport.setColumnSelection(cs);
alignPanel.paintAlignment(true);
- int columnCount = invert ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
- - bs.cardinality()
+ int columnCount = invert
+ ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
+ - bs.cardinality()
: bs.cardinality();
avcg.setStatus(MessageManager.formatMessage(
- "label.view_controller_toggled_marked",
- new String[] {
- toggle ? MessageManager.getString("label.toggled")
- : MessageManager.getString("label.marked"),
+ "label.view_controller_toggled_marked", new String[]
+ { toggle ? MessageManager.getString("label.toggled")
+ : MessageManager.getString("label.marked"),
String.valueOf(columnCount),
invert ? MessageManager
.getString("label.not_containing")
return that.mapping == null;
}
// TODO: can simplify by asserting fromSeq is a dataset sequence
- return (this.fromSeq == that.fromSeq || (this.fromSeq != null
- && that.fromSeq != null
- && this.fromSeq.getDatasetSequence() != null && this.fromSeq
- .getDatasetSequence() == that.fromSeq.getDatasetSequence()))
+ return (this.fromSeq == that.fromSeq
+ || (this.fromSeq != null && that.fromSeq != null
+ && this.fromSeq.getDatasetSequence() != null
+ && this.fromSeq.getDatasetSequence() == that.fromSeq
+ .getDatasetSequence()))
&& this.mapping.equals(that.mapping);
}
SequenceI fromSeq = (dnaseq.getDatasetSequence() == null) ? dnaseq
: dnaseq.getDatasetSequence();
- SequenceI toSeq = (aaseq.getDatasetSequence() == null) ? aaseq : aaseq
- .getDatasetSequence();
+ SequenceI toSeq = (aaseq.getDatasetSequence() == null) ? aaseq
+ : aaseq.getDatasetSequence();
/*
* if we already hold a mapping between these sequences, just add to it
{
SequenceI targetDs = target.getDatasetSequence() == null ? target
: target.getDatasetSequence();
- SequenceI queryDs = query.getDatasetSequence() == null ? query : query
- .getDatasetSequence();
+ SequenceI queryDs = query.getDatasetSequence() == null ? query
+ : query.getDatasetSequence();
if (targetDs == null || queryDs == null /*|| dnaToProt == null*/)
{
return null;
codonPos = MappingUtils.flattenRanges(codonPos);
char[] dna = dnaSeq.getSequence();
int start = dnaSeq.getStart();
- result.add(new char[] { dna[codonPos[0] - start],
- dna[codonPos[1] - start], dna[codonPos[2] - start] });
+ result.add(
+ new char[]
+ { dna[codonPos[0] - start], dna[codonPos[1] - start],
+ dna[codonPos[2] - start] });
}
}
return result.isEmpty() ? null : result;
*/
protected int realiseWith(SequenceI seq, boolean doUpdate)
{
- SequenceI ds = seq.getDatasetSequence() != null ? seq
- .getDatasetSequence() : seq;
+ SequenceI ds = seq.getDatasetSequence() != null
+ ? seq.getDatasetSequence()
+ : seq;
int count = 0;
/*
{
int start = replacement.getStart();
int end = replacement.getEnd();
- boolean mappingOverlapsSequence = (mapStart >= start && mapStart <= end)
- || (mapEnd >= start && mapEnd <= end);
+ boolean mappingOverlapsSequence = (mapStart >= start
+ && mapStart <= end) || (mapEnd >= start && mapEnd <= end);
if (mappingOverlapsSequence)
{
return true;
{
SequenceI dssFrom = fromSeq.getDatasetSequence() == null ? fromSeq
: fromSeq.getDatasetSequence();
- SequenceI dssTo = toSeq.getDatasetSequence() == null ? toSeq : toSeq
- .getDatasetSequence();
+ SequenceI dssTo = toSeq.getDatasetSequence() == null ? toSeq
+ : toSeq.getDatasetSequence();
for (SequenceToSequenceMapping mapping : mappings)
{
*/
public static AlignmentI createAlignment(CigarArray compactAlignment)
{
- throw new Error(
- MessageManager
- .getString("error.alignment_cigararray_not_implemented"));
+ throw new Error(MessageManager
+ .getString("error.alignment_cigararray_not_implemented"));
// this(compactAlignment.refCigars);
}
return AlignmentUtils.getSequencesByName(this);
}
-
@Override
public SequenceI getSequenceAt(int i)
{
return;
}
// remove annotation very quickly
- AlignmentAnnotation[] t, todelete = new AlignmentAnnotation[annotations.length], tokeep = new AlignmentAnnotation[annotations.length];
+ AlignmentAnnotation[] t,
+ todelete = new AlignmentAnnotation[annotations.length],
+ tokeep = new AlignmentAnnotation[annotations.length];
int i, p, k;
if (gp == null)
{
sqname = sq.getName();
if (sqname.equals(token) // exact match
|| (b && // allow imperfect matches - case varies
- (sqname.equalsIgnoreCase(token))))
+ (sqname.equalsIgnoreCase(token))))
{
return getSequenceAt(i);
}
return -1;
}
-
@Override
public int getHeight()
{
}
if (dbr.getMap().getTo().getDatasetSequence() != null)
{
- throw new Error(
- "Implementation error: Map.getTo() for dbref " + dbr
- + " from " + curDs.getName()
- + " is not a dataset sequence.");
+ throw new Error("Implementation error: Map.getTo() for dbref "
+ + dbr + " from " + curDs.getName()
+ + " is not a dataset sequence.");
}
// we recurse to add all forward references to dataset sequences via
// DBRefs/etc
current = getSequenceAt(i);
// This should really be a sequence method
ends[i * 2] = current.findIndex(current.getStart());
- ends[i * 2 + 1] = current.findIndex(current.getStart()
- + current.getLength());
+ ends[i * 2 + 1] = current
+ .findIndex(current.getStart() + current.getLength());
boolean hitres = false;
for (int j = 0, rs = 0, ssiz = current.getLength(); j < ssiz; j++)
{
boolean hashidden = toappend.getHiddenSequences() != null
&& toappend.getHiddenSequences().hiddenSequences != null;
// get all sequences including any hidden ones
- List<SequenceI> sqs = (hashidden) ? toappend.getHiddenSequences()
- .getFullAlignment().getSequences() : toappend.getSequences();
+ List<SequenceI> sqs = (hashidden)
+ ? toappend.getHiddenSequences().getFullAlignment()
+ .getSequences()
+ : toappend.getSequences();
if (sqs != null)
{
// avoid self append deadlock by
if (ourval instanceof String)
{
// append strings
- this.setProperty(k, ((String) ourval) + "; "
- + ((String) toapprop));
+ this.setProperty(k,
+ ((String) ourval) + "; " + ((String) toapprop));
}
else
{
{
for (AlignmentAnnotation a : alignmentAnnotation)
{
- if (a.getCalcId() == calcId
- || (a.getCalcId() != null && calcId != null && a
- .getCalcId().equals(calcId)))
+ if (a.getCalcId() == calcId || (a.getCalcId() != null
+ && calcId != null && a.getCalcId().equals(calcId)))
{
aa.add(a);
}
ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
for (AlignmentAnnotation ann : getAlignmentAnnotation())
{
- if ((calcId == null || (ann.getCalcId() != null && ann.getCalcId()
- .equals(calcId)))
- && (seq == null || (ann.sequenceRef != null && ann.sequenceRef == seq))
- && (label == null || (ann.label != null && ann.label
- .equals(label))))
+ if ((calcId == null || (ann.getCalcId() != null
+ && ann.getCalcId().equals(calcId)))
+ && (seq == null || (ann.sequenceRef != null
+ && ann.sequenceRef == seq))
+ && (label == null
+ || (ann.label != null && ann.label.equals(label))))
{
aa.add(ann);
}
firstChar = annotations[i].displayCharacter.charAt(0);
// check to see if it looks like a sequence or is secondary structure
// labelling.
- if (annotations[i].secondaryStructure != ' '
- && !hasIcons
- &&
- // Uncomment to only catch case where
- // displayCharacter==secondary
- // Structure
- // to correctly redisplay SS annotation imported from Stockholm,
- // exported to JalviewXML and read back in again.
- // &&
- // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
- firstChar != ' '
- && firstChar != '$'
- && firstChar != 0xCE
- && firstChar != '('
- && firstChar != '['
- && firstChar != '>'
- && firstChar != '{'
- && firstChar != 'A'
- && firstChar != 'B'
- && firstChar != 'C'
- && firstChar != 'D'
- && firstChar != 'E'
- && firstChar != 'F'
- && firstChar != 'G'
- && firstChar != 'H'
- && firstChar != 'I'
- && firstChar != 'J'
- && firstChar != 'K'
- && firstChar != 'L'
- && firstChar != 'M'
- && firstChar != 'N'
- && firstChar != 'O'
- && firstChar != 'P'
- && firstChar != 'Q'
- && firstChar != 'R'
- && firstChar != 'S'
- && firstChar != 'T'
- && firstChar != 'U'
- && firstChar != 'V'
- && firstChar != 'W'
- && firstChar != 'X'
- && firstChar != 'Y'
- && firstChar != 'Z'
+ if (annotations[i].secondaryStructure != ' ' && !hasIcons &&
+ // Uncomment to only catch case where
+ // displayCharacter==secondary
+ // Structure
+ // to correctly redisplay SS annotation imported from Stockholm,
+ // exported to JalviewXML and read back in again.
+ // &&
+ // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
+ firstChar != ' ' && firstChar != '$' && firstChar != 0xCE
+ && firstChar != '(' && firstChar != '[' && firstChar != '>'
+ && firstChar != '{' && firstChar != 'A' && firstChar != 'B'
+ && firstChar != 'C' && firstChar != 'D' && firstChar != 'E'
+ && firstChar != 'F' && firstChar != 'G' && firstChar != 'H'
+ && firstChar != 'I' && firstChar != 'J' && firstChar != 'K'
+ && firstChar != 'L' && firstChar != 'M' && firstChar != 'N'
+ && firstChar != 'O' && firstChar != 'P' && firstChar != 'Q'
+ && firstChar != 'R' && firstChar != 'S' && firstChar != 'T'
+ && firstChar != 'U' && firstChar != 'V' && firstChar != 'W'
+ && firstChar != 'X' && firstChar != 'Y' && firstChar != 'Z'
&& firstChar != '-'
&& firstChar < jalview.schemes.ResidueProperties.aaIndex.length)
{
{
return ((index + offset < 0) || (index + offset) >= max
|| annotations[index + offset] == null
- || (annotations[index + offset].secondaryStructure <= ' ') ? ' '
- : annotations[index + offset].displayCharacter == null
- || annotations[index + offset].displayCharacter
- .length() == 0 ? annotations[index + offset].secondaryStructure
- : annotations[index + offset].displayCharacter
- .charAt(0));
+ || (annotations[index + offset].secondaryStructure <= ' ')
+ ? ' '
+ : annotations[index + offset].displayCharacter == null
+ || annotations[index
+ + offset].displayCharacter
+ .length() == 0
+ ? annotations[index
+ + offset].secondaryStructure
+ : annotations[index
+ + offset].displayCharacter
+ .charAt(0));
}
@Override
for (int i = offset; i < mx; i++)
{
- string[i] = (annotations[i] == null || (annotations[i].secondaryStructure <= 32)) ? ' '
- : (annotations[i].displayCharacter == null
- || annotations[i].displayCharacter.length() == 0 ? annotations[i].secondaryStructure
- : annotations[i].displayCharacter.charAt(0));
+ string[i] = (annotations[i] == null
+ || (annotations[i].secondaryStructure <= 32))
+ ? ' '
+ : (annotations[i].displayCharacter == null
+ || annotations[i].displayCharacter
+ .length() == 0
+ ? annotations[i].secondaryStructure
+ : annotations[i].displayCharacter
+ .charAt(0));
}
return new String(string);
}
Annotation[] temp = new Annotation[endRes - startRes + 1];
if (startRes < annotations.length)
{
- System.arraycopy(annotations, startRes, temp, 0, endRes - startRes
- + 1);
+ System.arraycopy(annotations, startRes, temp, 0,
+ endRes - startRes + 1);
}
if (sequenceRef != null)
{
{
if (i + 1 < iSize)
{
- System.arraycopy(annotations, i + 1, annotations, i, iSize - i
- - 1);
+ System.arraycopy(annotations, i + 1, annotations, i,
+ iSize - i - 1);
}
iSize--;
}
{
if (sequenceRef != null)
{
- boolean rIsDs = sequenceRef.getDatasetSequence() == null, tIsDs = sequenceI
- .getDatasetSequence() == null;
+ boolean rIsDs = sequenceRef.getDatasetSequence() == null,
+ tIsDs = sequenceI.getDatasetSequence() == null;
if (sequenceRef != sequenceI
- && (rIsDs && !tIsDs && sequenceRef != sequenceI
- .getDatasetSequence())
- && (!rIsDs && tIsDs && sequenceRef.getDatasetSequence() != sequenceI)
- && (!rIsDs && !tIsDs && sequenceRef.getDatasetSequence() != sequenceI
- .getDatasetSequence())
+ && (rIsDs && !tIsDs
+ && sequenceRef != sequenceI.getDatasetSequence())
+ && (!rIsDs && tIsDs
+ && sequenceRef.getDatasetSequence() != sequenceI)
+ && (!rIsDs && !tIsDs
+ && sequenceRef.getDatasetSequence() != sequenceI
+ .getDatasetSequence())
&& !sequenceRef.equals(sequenceI))
{
// if sequenceRef isn't intersecting with sequenceI
throw new Error(
"liftOver currently not implemented for transfer of annotation between different types of seqeunce");
}
- boolean mapIsTo = (sp2sq != null) ? (sp2sq.getTo() == sq || sp2sq
- .getTo() == sq.getDatasetSequence()) : false;
+ boolean mapIsTo = (sp2sq != null)
+ ? (sp2sq.getTo() == sq
+ || sp2sq.getTo() == sq.getDatasetSequence())
+ : false;
// TODO build a better annotation element map and get rid of annotations[]
Map<Integer, Annotation> mapForsq = new HashMap<Integer, Annotation>();
{
for (Entry<Integer, Annotation> ie : sequenceMapping.entrySet())
{
- Integer mpos = Integer.valueOf(mapIsTo ? sp2sq
- .getMappedPosition(ie.getKey()) : sp2sq.getPosition(ie
- .getKey()));
+ Integer mpos = Integer
+ .valueOf(mapIsTo ? sp2sq.getMappedPosition(ie.getKey())
+ : sp2sq.getPosition(ie.getKey()));
if (mpos >= sq.getStart() && mpos <= sq.getEnd())
{
mapForsq.put(mpos, ie.getValue());
* up to and excluding the target column; if the count is less
* than 1, the opening bracket is unmatched, so return its match
*/
- String closer = String.valueOf(Rna
- .getMatchingClosingParenthesis(symbol));
+ String closer = String
+ .valueOf(Rna.getMatchingClosingParenthesis(symbol));
String opener = String.valueOf(symbol);
int count = 0;
for (int j = col + 1; j < column; j++)
{
if (!identity)
{
- throw new Error("Weak sequenceI equivalence not yet implemented.");
+ throw new Error(
+ "Weak sequenceI equivalence not yet implemented.");
}
else
{
}
if (!identity)
{
- throw new Error("Weak sequenceI equivalence not yet implemented.");
+ throw new Error(
+ "Weak sequenceI equivalence not yet implemented.");
}
else
{
* - when set, any groups on the given alignment will be marked on
* the view
*/
- public AlignmentView(AlignmentI alignment,
- HiddenColumns hidden,
- SequenceGroup selection,
- boolean hasHiddenColumns, boolean selectedRegionOnly,
- boolean recordGroups)
+ public AlignmentView(AlignmentI alignment, HiddenColumns hidden,
+ SequenceGroup selection, boolean hasHiddenColumns,
+ boolean selectedRegionOnly, boolean recordGroups)
{
// refactored from AlignViewport.getAlignmentView(selectedOnly);
this(new jalview.datamodel.CigarArray(alignment,
(hasHiddenColumns ? hidden : null),
(selectedRegionOnly ? selection : null)),
- (selectedRegionOnly && selection != null) ? selection
- .getStartRes() : 0);
+ (selectedRegionOnly && selection != null)
+ ? selection.getStartRes()
+ : 0);
isNa = alignment.isNucleotide();
// walk down SeqCigar array and Alignment Array - optionally restricted by
// selected region.
{
List<SequenceI> sel = selection.getSequences(null);
this.selected = new ScGroup();
- selseqs = selection
- .getSequencesInOrder(alignment, selectedRegionOnly);
+ selseqs = selection.getSequencesInOrder(alignment,
+ selectedRegionOnly);
}
else
{
{
HiddenColumns hidden = new HiddenColumns();
- return new Object[] {
- SeqCigar.createAlignmentSequences(sequences, gapCharacter, hidden,
- contigs), hidden };
+ return new Object[] { SeqCigar.createAlignmentSequences(sequences,
+ gapCharacter, hidden, contigs),
+ hidden };
}
/**
* - true if vcal is alignment of the visible regions of the view
* (e.g. as returned from getVisibleAlignment)
*/
- private void addPrunedGroupsInOrder(AlignmentI vcal, int gstart,
- int gend, boolean viscontigs)
+ private void addPrunedGroupsInOrder(AlignmentI vcal, int gstart, int gend,
+ boolean viscontigs)
{
boolean r = false;
if (gstart > -1 && gstart <= gend)
for (int h = 0; h < contigs.length; h += 3)
{
{
- prune.addShift(p + contigs[h + 1], contigs[h + 2]
- - contigs[h + 1]);
+ prune.addShift(p + contigs[h + 1],
+ contigs[h + 2] - contigs[h + 1]);
}
p = contigs[h + 1] + contigs[h + 2];
}
SequenceI mseq[] = new SequenceI[sequences.length];
for (int s = 0; s < mseq.length; s++)
{
- mseq[s] = sequences[s].getSeq(gapCharacter).getSubSequence(
- start, contigs[contig + 1]);
+ mseq[s] = sequences[s].getSeq(gapCharacter)
+ .getSubSequence(start, contigs[contig + 1]);
}
smsa[j] = mseq;
j++;
{
if (sequences == null || width <= 0)
{
- throw new Error(
- MessageManager
- .getString("error.empty_view_cannot_be_updated"));
+ throw new Error(MessageManager
+ .getString("error.empty_view_cannot_be_updated"));
}
if (nvismsa == null)
{
j++;
if (mseq.length != sequences.length)
{
- throw new Error(
- MessageManager
- .formatMessage(
- "error.mismatch_between_number_of_sequences_in_block",
- new String[] {
- Integer.valueOf(j).toString(),
- Integer.valueOf(mseq.length)
- .toString(),
- Integer.valueOf(
- sequences.length)
- .toString() }));
+ throw new Error(MessageManager.formatMessage(
+ "error.mismatch_between_number_of_sequences_in_block",
+ new String[]
+ { Integer.valueOf(j).toString(),
+ Integer.valueOf(mseq.length).toString(),
+ Integer.valueOf(sequences.length)
+ .toString() }));
}
swidth = mseq[0].getLength(); // JBPNote: could ensure padded
// here.
}
else
{
- alignment[s].setSequence(alignment[s]
- .getSequenceAsString()
- + mseq[s].getSequenceAsString());
+ alignment[s]
+ .setSequence(alignment[s].getSequenceAsString()
+ + mseq[s].getSequenceAsString());
if (mseq[s].getStart() <= mseq[s].getEnd())
{
alignment[s].setEnd(mseq[s].getEnd());
}
else
{
- alignment[s].setSequence(alignment[s]
- .getSequenceAsString()
- + oseq.getSequenceAsString());
+ alignment[s]
+ .setSequence(alignment[s].getSequenceAsString()
+ + oseq.getSequenceAsString());
if (oseq.getEnd() >= oseq.getStart())
{
alignment[s].setEnd(oseq.getEnd());
}
}
// mark hidden segment as hidden in the new alignment
- hidden.hideColumns(nwidth, nwidth + contigs[contig + 2]
- - 1);
+ hidden.hideColumns(nwidth, nwidth + contigs[contig + 2] - 1);
nwidth += contigs[contig + 2];
}
// Do final segment - if it exists
}
else
{
- alignment[s].setSequence(alignment[s]
- .getSequenceAsString()
- + oseq.getSequenceAsString());
+ alignment[s]
+ .setSequence(alignment[s].getSequenceAsString()
+ + oseq.getSequenceAsString());
if (oseq.getEnd() >= oseq.getStart())
{
alignment[s].setEnd(oseq.getEnd());
else
{
// place gaps.
- throw new Error(
- MessageManager
- .getString("error.padding_not_yet_implemented"));
+ throw new Error(MessageManager
+ .getString("error.padding_not_yet_implemented"));
}
}
}
{
if (nvismsa.length != 1)
{
- throw new Error(
- MessageManager
- .formatMessage(
- "error.mismatch_between_visible_blocks_to_update_and_number_of_contigs_in_view",
- new String[] { Integer.valueOf(
- nvismsa.length).toString() }));
+ throw new Error(MessageManager.formatMessage(
+ "error.mismatch_between_visible_blocks_to_update_and_number_of_contigs_in_view",
+ new String[]
+ { Integer.valueOf(nvismsa.length).toString() }));
}
if (nvismsa[0] != null)
{
AlignmentView view = null;
try
{
- System.out
- .println("View with no hidden columns, no limit to selection, no groups to be collected:");
+ System.out.println(
+ "View with no hidden columns, no limit to selection, no groups to be collected:");
view = new AlignmentView(alignment, hidden, selection, false, false,
false);
summariseAlignmentView(view, System.out);
} catch (Exception e)
{
e.printStackTrace();
- System.err
- .println("Failed to generate alignment with selection but no groups marked.");
+ System.err.println(
+ "Failed to generate alignment with selection but no groups marked.");
}
try
{
- System.out
- .println("View with no hidden columns, no limit to selection, and all groups to be collected:");
+ System.out.println(
+ "View with no hidden columns, no limit to selection, and all groups to be collected:");
view = new AlignmentView(alignment, hidden, selection, false, false,
true);
summariseAlignmentView(view, System.out);
} catch (Exception e)
{
e.printStackTrace();
- System.err
- .println("Failed to generate alignment with selection marked but no groups marked.");
+ System.err.println(
+ "Failed to generate alignment with selection marked but no groups marked.");
}
try
{
- System.out
- .println("View with no hidden columns, limited to selection and no groups to be collected:");
+ System.out.println(
+ "View with no hidden columns, limited to selection and no groups to be collected:");
view = new AlignmentView(alignment, hidden, selection, false, true,
false);
summariseAlignmentView(view, System.out);
} catch (Exception e)
{
e.printStackTrace();
- System.err
- .println("Failed to generate alignment with selection restricted but no groups marked.");
+ System.err.println(
+ "Failed to generate alignment with selection restricted but no groups marked.");
}
try
{
- System.out
- .println("View with no hidden columns, limited to selection, and all groups to be collected:");
+ System.out.println(
+ "View with no hidden columns, limited to selection, and all groups to be collected:");
view = new AlignmentView(alignment, hidden, selection, false, true,
true);
summariseAlignmentView(view, System.out);
} catch (Exception e)
{
e.printStackTrace();
- System.err
- .println("Failed to generate alignment with selection restricted and groups marked.");
+ System.err.println(
+ "Failed to generate alignment with selection restricted and groups marked.");
}
try
{
- System.out
- .println("View *with* hidden columns, no limit to selection, no groups to be collected:");
+ System.out.println(
+ "View *with* hidden columns, no limit to selection, no groups to be collected:");
view = new AlignmentView(alignment, hidden, selection, true, false,
false);
summariseAlignmentView(view, System.out);
} catch (Exception e)
{
e.printStackTrace();
- System.err
- .println("Failed to generate alignment with selection but no groups marked.");
+ System.err.println(
+ "Failed to generate alignment with selection but no groups marked.");
}
try
{
- System.out
- .println("View *with* hidden columns, no limit to selection, and all groups to be collected:");
+ System.out.println(
+ "View *with* hidden columns, no limit to selection, and all groups to be collected:");
view = new AlignmentView(alignment, hidden, selection, true, false,
true);
summariseAlignmentView(view, System.out);
} catch (Exception e)
{
e.printStackTrace();
- System.err
- .println("Failed to generate alignment with selection marked but no groups marked.");
+ System.err.println(
+ "Failed to generate alignment with selection marked but no groups marked.");
}
try
{
- System.out
- .println("View *with* hidden columns, limited to selection and no groups to be collected:");
+ System.out.println(
+ "View *with* hidden columns, limited to selection and no groups to be collected:");
view = new AlignmentView(alignment, hidden, selection, true, true,
false);
summariseAlignmentView(view, System.out);
} catch (Exception e)
{
e.printStackTrace();
- System.err
- .println("Failed to generate alignment with selection restricted but no groups marked.");
+ System.err.println(
+ "Failed to generate alignment with selection restricted but no groups marked.");
}
try
{
- System.out
- .println("View *with* hidden columns, limited to selection, and all groups to be collected:");
+ System.out.println(
+ "View *with* hidden columns, limited to selection, and all groups to be collected:");
view = new AlignmentView(alignment, hidden, selection, true, true,
true);
summariseAlignmentView(view, System.out);
} catch (Exception e)
{
e.printStackTrace();
- System.err
- .println("Failed to generate alignment with selection restricted and groups marked.");
+ System.err.println(
+ "Failed to generate alignment with selection restricted and groups marked.");
}
}
public class AllColsCollection implements AlignmentColsCollectionI
{
int start;
+
int end;
HiddenColumns hidden;
-
+
public AllColsCollection(int s, int e, AlignmentI al)
{
start = s;
end = e;
hidden = al.getHiddenColumns();
}
-
+
@Override
public Iterator<Integer> iterator()
{
- return new AllColsIterator(start,end,hidden);
+ return new AllColsIterator(start, end, hidden);
}
@Override
private int current;
- public AllColsIterator(int firstcol, int lastcol, HiddenColumns hiddenCols)
+ public AllColsIterator(int firstcol, int lastcol,
+ HiddenColumns hiddenCols)
{
last = lastcol;
next = firstcol;
throw new UnsupportedOperationException();
}
}
-
return alignment.getSequenceAtAbsoluteIndex(seq);
}
}
-
throw new UnsupportedOperationException();
}
}
-
-
*/
public char secondaryStructure = ' ';
- /** Score for the position - used in histograms, line graphs and for shading */
+ /**
+ * Score for the position - used in histograms, line graphs and for shading
+ */
public float value;
/** Colour for position */
public boolean isWhitespace()
{
return ((value == 0f)
- && ((description == null) || (description.trim()
- .length() == 0))
- && ((displayCharacter == null) || (displayCharacter
- .trim().length() == 0))
- && (secondaryStructure == '\0' || (secondaryStructure == ' ')) && colour == null);
+ && ((description == null) || (description.trim().length() == 0))
+ && ((displayCharacter == null)
+ || (displayCharacter.trim().length() == 0))
+ && (secondaryStructure == '\0' || (secondaryStructure == ' '))
+ && colour == null);
}
}
*
* set the display name
*
- * @param new name
+ * @param new
+ * name
*/
public void setName(String name)
{
{
if (isNa != smtrx.isDNA())
{
- throw new InvalidSequenceTypeException("matrix "
- + smtrx.getClass().getCanonicalName()
- + " is not a valid matrix for "
- + (isNa ? "nucleotide" : "protein") + "sequences");
+ throw new InvalidSequenceTypeException(
+ "matrix " + smtrx.getClass().getCanonicalName()
+ + " is not a valid matrix for "
+ + (isNa ? "nucleotide" : "protein") + "sequences");
}
matrixEncode(smtrx.isDNA() ? ResidueProperties.nucleotideIndex
: ResidueProperties.aaIndex, smtrx.getMatrix());
for (int c = 0; c < cigars.length; c++)
{
refCigars[c] = cigars[c];
- if (!((cigars[c] instanceof SeqCigar) || cigars[c] instanceof CigarCigar))
+ if (!((cigars[c] instanceof SeqCigar)
+ || cigars[c] instanceof CigarCigar))
{
seqcigararray = false;
}
{
this(constructSeqCigarArray(alignment, selectionGroup));
constructFromAlignment(alignment,
- hidden != null ? hidden.getHiddenColumnsCopy()
- : null, selectionGroup);
+ hidden != null ? hidden.getHiddenColumnsCopy() : null,
+ selectionGroup);
}
private static int[] _calcStartEndBounds(AlignmentI alignment,
int[][] deletions = new int[length][];
int[][] trunc_deletions = null;
StringBuffer sq = new StringBuffer();
- int cursor = 0, alcursor = 0, start = 0, startpos = 0, end = 0, endpos = 0, delcount = -1;
+ int cursor = 0, alcursor = 0, start = 0, startpos = 0, end = 0,
+ endpos = 0, delcount = -1;
boolean consecutive_del = false;
if (length == 0)
{
break;
default:
throw new Error(MessageManager.formatMessage(
- "error.unknown_seq_cigar_operation",
- new String[] { new StringBuffer(operation[i]).toString() }));
+ "error.unknown_seq_cigar_operation", new String[]
+ { new StringBuffer(operation[i]).toString() }));
}
}
if (++delcount > 0)
}
deletions = null;
return new Object[] { ((reference != null) ? sq.toString() : null),
- new int[] { start, startpos, end, endpos }, trunc_deletions };
+ new int[]
+ { start, startpos, end, endpos }, trunc_deletions };
}
protected void compact_operations()
} while (c >= '0' && c <= '9' && j < l);
if (j >= l && c >= '0' && c <= '9')
{
- throw new Exception(
- MessageManager
- .getString("exception.unterminated_cigar_string"));
+ throw new Exception(MessageManager
+ .getString("exception.unterminated_cigar_string"));
}
try
{
i = j;
} catch (Exception e)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_bug_parse_cigar_string"));
+ throw new Error(MessageManager
+ .getString("error.implementation_bug_parse_cigar_string"));
}
if (c >= 'a' && c <= 'z')
{
{
throw new Exception(MessageManager.formatMessage(
"exception.unexpected_operation_cigar_string_pos",
- new String[] { new StringBuffer(c).toString(),
+ new String[]
+ { new StringBuffer(c).toString(),
Integer.valueOf(i).toString(), cigarString }));
}
}
}
if (op != M && op != D && op != I)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_invalid_operation_string"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_invalid_operation_string"));
}
if (range == 0)
{
* int public void addOperationAt(int pos, char op, int range) { int
* cursor = -1; // mark the position for the current operation being
* edited. int o = 0; boolean last_d = false; // previous op was a
- * deletion. if (pos < -1) throw new
- * Error("pos<-1 is not supported."); while (o<length) { if
- * (operation[o] != D) { if ( (cursor + this.range[o]) < pos) {
- * cursor += this.range[o]; o++; last_d=false; } else { break; } }
- * else { last_d=true; o++; } } if (o==length) { // must insert more
- * operations before pos if (pos-cursor>0) addInsertion(pos-cursor);
- * // then just add the new operation. Regardless of what it is.
- * addOperation(op, range); } else { int diff = pos - cursor;
+ * deletion. if (pos < -1) throw new Error("pos<-1 is not
+ * supported."); while (o<length) { if (operation[o] != D) { if (
+ * (cursor + this.range[o]) < pos) { cursor += this.range[o]; o++;
+ * last_d=false; } else { break; } } else { last_d=true; o++; } } if
+ * (o==length) { // must insert more operations before pos if
+ * (pos-cursor>0) addInsertion(pos-cursor); // then just add the new
+ * operation. Regardless of what it is. addOperation(op, range); }
+ * else { int diff = pos - cursor;
*
* int e_length = length-o; // new edit operation array length. //
* diff<0 - can only happen before first insertion or match. -
}
if (start < 0 || start > end)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_delete_range_out_of_bounds"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_delete_range_out_of_bounds"));
}
// find beginning
int cursor = 0; // mark the position for the current operation being edited.
default:
throw new Error(MessageManager.formatMessage(
"error.implementation_error_unknown_operation",
- new String[] { new StringBuffer(oldops[o]).toString() }));
+ new String[]
+ { new StringBuffer(oldops[o]).toString() }));
}
rlength -= remain;
remain = oldrange[++o]; // number of op characters left to edit
String refString = refCigar.getSequenceString(GapChar);
if (refString != null)
{
- return (length == 0) ? "" : (String) getSequenceAndDeletions(
- refString, GapChar)[0];
+ return (length == 0) ? ""
+ : (String) getSequenceAndDeletions(refString, GapChar)[0];
}
else
{
}
-
/**
* Hides the specified column and any adjacent selected columns
*
hidden.hideColumns(min, max);
}
-
-
-
-
/**
* Copy constructor
*
{
}
-
-
-
-
-
/**
* Invert the column selection from first to end-1. leaves hiddenColumns
* untouched (and unselected)
}
}
-
/**
*
* @return true if there are columns marked
return (selection != null && selection.size() > 0);
}
-
-
public boolean filterAnnotations(Annotation[] annotations,
AnnotationFilterParameter filterParams)
{
boolean itemMatched = false;
- if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD
+ if (filterParams
+ .getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD
&& annotations[count].value >= filterParams
.getThresholdValue())
{
itemMatched = true;
}
- if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD
+ if (filterParams
+ .getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD
&& annotations[count].value <= filterParams
.getThresholdValue())
{
*
* @return
*/
- public boolean markColumns(BitSet markedColumns, int startCol,
- int endCol, boolean invert, boolean extendCurrent, boolean toggle)
+ public boolean markColumns(BitSet markedColumns, int startCol, int endCol,
+ boolean invert, boolean extendCurrent, boolean toggle)
{
boolean changed = false;
if (!extendCurrent && !toggle)
public DBRefEntry(DBRefEntryI entry)
{
this((entry.getSource() == null ? "" : new String(entry.getSource())),
- (entry.getVersion() == null ? "" : new String(
- entry.getVersion())),
- (entry.getAccessionId() == null ? "" : new String(
- entry.getAccessionId())),
+ (entry.getVersion() == null ? ""
+ : new String(entry.getVersion())),
+ (entry.getAccessionId() == null ? ""
+ : new String(entry.getAccessionId())),
(entry.getMap() == null ? null : new Mapping(entry.getMap())));
}
{
return true;
}
- if (equalRef(entry)
- && ((map == null && entry.map == null) || (map != null
- && entry.map != null && map.equals(entry.map))))
+ if (equalRef(entry) && ((map == null && entry.map == null)
+ || (map != null && entry.map != null && map.equals(entry.map))))
{
return true;
}
* <ul>
* <li>source and accession are identical (ignoring case)</li>
* <li>version is identical (ignoring case), or this version is of the format
- * "someSource:0", in which case the version for the other entry replaces it</li>
+ * "someSource:0", in which case the version for the other entry replaces
+ * it</li>
* <li>mappings are not compared but if this entry has no mapping, replace
* with that for the other entry</li>
* </ul>
String otherAccession = other.getAccessionId();
if ((accessionId == null && otherAccession != null)
|| (accessionId != null && otherAccession == null)
- || (accessionId != null && !accessionId
- .equalsIgnoreCase(otherAccession)))
+ || (accessionId != null
+ && !accessionId.equalsIgnoreCase(otherAccession)))
{
return false;
}
}
else
{
- if (version != null
- && (otherVersion == null || !version
- .equalsIgnoreCase(otherVersion)))
+ if (version != null && (otherVersion == null
+ || !version.equalsIgnoreCase(otherVersion)))
{
return false;
}
return true;
}
if (entry != null
- && (source != null && entry.getSource() != null && source
- .equalsIgnoreCase(entry.getSource()))
- && (accessionId != null && entry.getAccessionId() != null && accessionId
- .equalsIgnoreCase(entry.getAccessionId()))
- && (version != null && entry.getVersion() != null && version
- .equalsIgnoreCase(entry.getVersion())))
+ && (source != null && entry.getSource() != null
+ && source.equalsIgnoreCase(entry.getSource()))
+ && (accessionId != null && entry.getAccessionId() != null
+ && accessionId.equalsIgnoreCase(entry.getAccessionId()))
+ && (version != null && entry.getVersion() != null
+ && version.equalsIgnoreCase(entry.getVersion())))
{
return true;
}
if (type.equalsIgnoreCase(EMBL_CODING_FEATURE))
{
return (dbrefsource == null
- || dbrefsource.equalsIgnoreCase(DBRefSource.EMBL) || dbrefsource
- .equalsIgnoreCase(DBRefSource.EMBLCDS));
+ || dbrefsource.equalsIgnoreCase(DBRefSource.EMBL)
+ || dbrefsource.equalsIgnoreCase(DBRefSource.EMBLCDS));
}
return false;
}
if (obj != null && obj instanceof GraphLine)
{
GraphLine other = (GraphLine) obj;
- return displayed == other.displayed
- && value == other.value
- && (colour != null ? (other.colour != null && other.colour
- .equals(colour)) : other.colour == null)
- && (label != null ? (other.label != null && other.label
- .equals(label)) : other.label == null);
+ return displayed == other.displayed && value == other.value
+ && (colour != null
+ ? (other.colour != null
+ && other.colour.equals(colour))
+ : other.colour == null)
+ && (label != null
+ ? (other.label != null && other.label.equals(label))
+ : other.label == null);
}
return false;
}
public class HiddenColumns
{
private static final ReentrantReadWriteLock LOCK = new ReentrantReadWriteLock();
-
+
/*
* list of hidden column [start, end] ranges; the list is maintained in
* ascending start column order
}
}
return size;
- }
- finally
+ } finally
{
LOCK.readLock().unlock();
}
{
LOCK.readLock().lock();
- int distance = visibleDistance;
+ int distance = visibleDistance;
- // in case startColumn is in a hidden region, move it to the left
- int start = adjustForHiddenColumns(findColumnPosition(startColumn));
+ // in case startColumn is in a hidden region, move it to the left
+ int start = adjustForHiddenColumns(findColumnPosition(startColumn));
- // get index of hidden region to left of start
- int index = getHiddenIndexLeft(start);
- if (index == -1)
- {
- // no hidden regions to left of startColumn
- return start - distance;
- }
+ // get index of hidden region to left of start
+ int index = getHiddenIndexLeft(start);
+ if (index == -1)
+ {
+ // no hidden regions to left of startColumn
+ return start - distance;
+ }
- // walk backwards through the alignment subtracting the counts of visible
- // columns from distance
- int[] region;
- int gap = 0;
- int nextstart = start;
+ // walk backwards through the alignment subtracting the counts of visible
+ // columns from distance
+ int[] region;
+ int gap = 0;
+ int nextstart = start;
- while ((index > -1) && (distance - gap > 0))
- {
- // subtract the gap to right of region from distance
- distance -= gap;
- start = nextstart;
+ while ((index > -1) && (distance - gap > 0))
+ {
+ // subtract the gap to right of region from distance
+ distance -= gap;
+ start = nextstart;
- // calculate the next gap
- region = hiddenColumns.get(index);
- gap = start - region[1];
+ // calculate the next gap
+ region = hiddenColumns.get(index);
+ gap = start - region[1];
- // set start to just to left of current region
- nextstart = region[0] - 1;
- index--;
- }
+ // set start to just to left of current region
+ nextstart = region[0] - 1;
+ index--;
+ }
- if (distance - gap > 0)
- {
- // fell out of loop because there are no more hidden regions
- distance -= gap;
- return nextstart - distance;
- }
- return start - distance;
+ if (distance - gap > 0)
+ {
+ // fell out of loop because there are no more hidden regions
+ distance -= gap;
+ return nextstart - distance;
+ }
+ return start - distance;
} finally
{
LOCK.readLock().unlock();
}
return positions;
- }
- finally
+ } finally
{
LOCK.readLock().unlock();
}
{
LOCK.readLock().lock();
- if (hiddenColumns != null)
- {
- int index = hiddenColumns.size() - 1;
- do
+ if (hiddenColumns != null)
{
- int[] region = hiddenColumns.get(index);
- if (alPos > region[1])
+ int index = hiddenColumns.size() - 1;
+ do
{
- return region[1];
- }
+ int[] region = hiddenColumns.get(index);
+ if (alPos > region[1])
+ {
+ return region[1];
+ }
- index--;
- } while (index > -1);
- }
+ index--;
+ } while (index > -1);
+ }
- return alPos;
+ return alPos;
} finally
{
LOCK.readLock().unlock();
{
LOCK.readLock().lock();
- if (hiddenColumns != null)
- {
- int index = hiddenColumns.size() - 1;
- do
+ if (hiddenColumns != null)
{
- int[] region = hiddenColumns.get(index);
- if (pos > region[1])
+ int index = hiddenColumns.size() - 1;
+ do
{
- return index;
- }
+ int[] region = hiddenColumns.get(index);
+ if (pos > region[1])
+ {
+ return index;
+ }
- index--;
- } while (index > -1);
- }
+ index--;
+ } while (index > -1);
+ }
- return -1;
+ return -1;
} finally
{
LOCK.readLock().unlock();
}
return;
}
- }
+ }
- /*
- * remaining case is that the new range follows everything else
- */
+ /*
+ * remaining case is that the new range follows everything else
+ */
hiddenColumns.add(new int[] { start, end });
} finally
{
{
LOCK.readLock().lock();
- if (hiddenColumns != null)
- {
- for (int[] region : hiddenColumns)
+ if (hiddenColumns != null)
{
- if (column >= region[0] && column <= region[1])
+ for (int[] region : hiddenColumns)
{
- return false;
+ if (column >= region[0] && column <= region[1])
+ {
+ return false;
+ }
}
}
- }
- return true;
+ return true;
} finally
{
LOCK.readLock().unlock();
return copy;
}
-
+
/**
* Returns a copy of the vector of hidden regions, as an ArrayList. Before
* using this method please consider if you really need access to the hidden
}
}
}
- }
- finally
+ } finally
{
LOCK.writeLock().unlock();
}
{
return new int[] { start, end - 1 };
}
- }
- finally
+ } finally
{
LOCK.readLock().unlock();
}
}
return selections;
- }
- finally
+ } finally
{
LOCK.readLock().unlock();
}
}
// otherwise, sequence was completely hidden
return new int[] { visPrev, visNext, 0, 0, firstP, lastP };
- }
- finally
+ } finally
{
LOCK.readLock().unlock();
}
{
alignmentAnnotation.restrict(start, end);
}
- }
- finally
+ } finally
{
LOCK.readLock().unlock();
}
}
hiddenColumns = null;
- }
- finally
+ } finally
{
LOCK.writeLock().unlock();
}
{
hiddenColumns = null;
}
- }
- finally
+ } finally
{
LOCK.writeLock().unlock();
}
hiddenColumns = null;
}
}
- }
- finally
+ } finally
{
LOCK.writeLock().unlock();
}
}
else
{
- al.getSequenceAt(s).setSequence(
- sq.substring(0, spos + offset) + sb.toString()
- + sq.substring(spos + offset));
+ al.getSequenceAt(s).setSequence(sq.substring(0, spos + offset)
+ + sb.toString() + sq.substring(spos + offset));
}
}
}
{
// pad the final region with gaps.
StringBuffer sb = new StringBuffer();
- for (int s = 0, ns = profileseq.getLength() - spos - offset; s < ns; s++)
+ for (int s = 0, ns = profileseq.getLength() - spos
+ - offset; s < ns; s++)
{
sb.append(gc);
}
}
}
return hashCode;
- }
- finally
+ } finally
{
LOCK.readLock().unlock();
}
{
inserts.set(range[0], range[1] + 1);
}
- }
- finally
+ } finally
{
LOCK.readLock().unlock();
}
}
else
{
- System.out.println(seq.getName()
- + " has been deleted whilst hidden");
+ System.out.println(
+ seq.getName() + " has been deleted whilst hidden");
}
}
}
}
if (!toRanges.hasNext())
{
- throw new NoSuchElementException("Ran out of peptide at position "
- + toPosition);
+ throw new NoSuchElementException(
+ "Ran out of peptide at position " + toPosition);
}
currentToRange = toRanges.next();
toPosition = currentToRange[0];
to[f * 2] = r[0];
to[f * 2 + 1] = r[1];
}
- copy.setMap(new MapList(from, to, map.getFromRatio(), map
- .getToRatio()));
+ copy.setMap(
+ new MapList(from, to, map.getFromRatio(), map.getToRatio()));
}
return copy;
}
* @param gapChar
* @return
*/
- public Iterator<AlignedCodon> getCodonIterator(SequenceI seq, char gapChar)
+ public Iterator<AlignedCodon> getCodonIterator(SequenceI seq,
+ char gapChar)
{
return new AlignedCodonIterator(seq, gapChar);
}
@Override
public String toString()
{
- return String.format("%s %s", this.map.toString(), this.to == null ? ""
- : this.to.getName());
+ return String.format("%s %s", this.map.toString(),
+ this.to == null ? "" : this.to.getName());
}
/**
{
return format;
}
+
public String getExtension()
{
return ext;
{
}
-
public PDBEntry(String pdbId, String chain, PDBEntry.Type type,
String filePath)
{
* @param entryType
* @param filePath
*/
- void init(String pdbId, String chain, PDBEntry.Type entryType, String filePath)
+ void init(String pdbId, String chain, PDBEntry.Type entryType,
+ String filePath)
{
this.id = pdbId;
this.type = entryType == null ? null : entryType.toString();
{
if (!DBRefSource.PDB.equals(dbr.getSource()))
{
- throw new IllegalArgumentException("Invalid source: "
- + dbr.getSource());
+ throw new IllegalArgumentException(
+ "Invalid source: " + dbr.getSource());
}
String pdbId = dbr.getAccessionId();
*/
package jalview.datamodel;
-
/**
* A profile for one column of an alignment
*
@Override
public ProfileI get(int col)
{
- return profiles != null && col >= 0 && col < profiles.length ? profiles[col]
+ return profiles != null && col >= 0 && col < profiles.length
+ ? profiles[col]
: null;
}
/**
* A class to count occurrences of residues in a profile, optimised for speed
* and memory footprint.
+ *
* @author gmcarstairs
*
*/
{
if (intCounts[i] == count)
{
- modal.append(isNucleotide ? NUCS.charAt(i - 1) : AAS
- .charAt(i - 1));
+ modal.append(
+ isNucleotide ? NUCS.charAt(i - 1) : AAS.charAt(i - 1));
}
}
}
{
if (counts[i] == count)
{
- modal.append(isNucleotide ? NUCS.charAt(i - 1) : AAS
- .charAt(i - 1));
+ modal.append(
+ isNucleotide ? NUCS.charAt(i - 1) : AAS.charAt(i - 1));
}
}
}
*
* @return
*/
- public int size() {
+ public int size()
+ {
int size = 0;
if (useIntCounts)
{
{
if (intCounts[i] > 0)
{
- char symbol = isNucleotide ? NUCS.charAt(i - 1) : AAS
- .charAt(i - 1);
+ char symbol = isNucleotide ? NUCS.charAt(i - 1)
+ : AAS.charAt(i - 1);
symbols[j] = symbol;
values[j] = intCounts[i];
j++;
{
if (counts[i] > 0)
{
- char symbol = isNucleotide ? NUCS.charAt(i - 1) : AAS
- .charAt(i - 1);
+ char symbol = isNucleotide ? NUCS.charAt(i - 1)
+ : AAS.charAt(i - 1);
symbols[j] = symbol;
values[j] = counts[i];
j++;
return false;
}
SearchResultMatchI m = (SearchResultMatchI) obj;
- return (sequence == m.getSequence() && start == m.getStart() && end == m
- .getEnd());
+ return (sequence == m.getSequence() && start == m.getStart()
+ && end == m.getEnd());
}
}
else
{
// debug
- // System.err.println("Outwith bounds!" + matchStart+">"+end +" or "
+ // System.err.println("Outwith bounds!" + matchStart+">"+end +" or "
// + matchEnd+"<"+start);
}
}
@Override
public String getSequenceString(char GapChar)
{
- return (length == 0) ? "" : (String) getSequenceAndDeletions(
- refseq.getSequenceAsString(start, end), GapChar)[0];
+ return (length == 0) ? ""
+ : (String) getSequenceAndDeletions(
+ refseq.getSequenceAsString(start, end), GapChar)[0];
}
/**
refseq.getSequenceAsString(start, end), GapChar);
if (edit_result == null)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_unexpected_null_from_get_sequence_and_deletions"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_unexpected_null_from_get_sequence_and_deletions"));
}
int bounds[] = (int[]) edit_result[1];
seq = new Sequence(refseq.getName(), (String) edit_result[0],
- refseq.getStart() + start + bounds[0], refseq.getStart()
- + start + ((bounds[2] == 0) ? -1 : bounds[2]));
+ refseq.getStart() + start + bounds[0], refseq.getStart() + start
+ + ((bounds[2] == 0) ? -1 : bounds[2]));
seq.setDescription(refseq.getDescription());
int sstart = seq.getStart(), send = seq.getEnd();
// seq.checkValidRange(); probably not needed
boolean hasgaps = false;
if (seq == null)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_set_seq_null"));
+ throw new Error(MessageManager
+ .getString("error.implementation_error_set_seq_null"));
}
if (_s < 0)
{
- throw new Error(MessageManager.formatMessage(
- "error.implementation_error_s", new String[] { Integer
- .valueOf(_s).toString() }));
+ throw new Error(MessageManager
+ .formatMessage("error.implementation_error_s", new String[]
+ { Integer.valueOf(_s).toString() }));
}
String seq_string = seq.getSequenceAsString();
if (_e == 0 || _e < _s || _e > seq_string.length())
// Check offsets
if (end > ds.getLength())
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_seqcigar_possible"));
+ throw new Error(MessageManager
+ .getString("error.implementation_error_seqcigar_possible"));
// end = ds.getLength();
}
}
if (operation.length != range.length)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_bug_cigar_operation_list_range_list"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_bug_cigar_operation_list_range_list"));
}
if (operation != null)
if (_setSeq(seq, false, 0, 0))
{
- throw new Error(
- MessageManager
- .getString("error.not_yet_implemented_cigar_object_from_cigar_string"));
+ throw new Error(MessageManager.getString(
+ "error.not_yet_implemented_cigar_object_from_cigar_string"));
}
for (int i = this.length, j = 0; j < operation.length; i++, j++)
{
if (op != M && op != I && op != D)
{
throw new Error(MessageManager.formatMessage(
- "error.implementation_bug_cigar_operation", new String[] {
- Integer.valueOf(j).toString(),
+ "error.implementation_bug_cigar_operation", new String[]
+ { Integer.valueOf(j).toString(),
Integer.valueOf(op).toString(),
Integer.valueOf(M).toString(),
Integer.valueOf(I).toString(),
this.length = 0;
if (_setSeq(seq, false, 0, 0))
{
- throw new Error(
- MessageManager
- .getString("error.not_yet_implemented_cigar_object_from_cigar_string"));
+ throw new Error(MessageManager.getString(
+ "error.not_yet_implemented_cigar_object_from_cigar_string"));
}
}
}
while (p <= endpos)
{
- boolean isGap = (p < res) ? jalview.util.Comparison.isGap(seq
- .getCharAt(p)) : true;
+ boolean isGap = (p < res)
+ ? jalview.util.Comparison.isGap(seq.getCharAt(p))
+ : true;
if ((startpos <= p) && (p <= endpos))
{
if (isGap)
super();
if (seq == null)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_for_new_cigar"));
+ throw new Error(MessageManager
+ .getString("error.implementation_error_for_new_cigar"));
}
_setSeq(seq, false, 0, 0);
// there is still work to do
super();
if (seq == null)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_for_new_cigar"));
+ throw new Error(MessageManager
+ .getString("error.implementation_error_for_new_cigar"));
}
_setSeq(seq, false, start, end + 1);
// there is still work to do
Object[] gs_regions = new Object[alseqs.length];
for (int i = 0; i < alseqs.length; i++)
{
- alseqs_string[i] = alseqs[i].getRefSeq().getSequenceAsString(
- alseqs[i].start, alseqs[i].end);
+ alseqs_string[i] = alseqs[i].getRefSeq()
+ .getSequenceAsString(alseqs[i].start, alseqs[i].end);
gs_regions[i] = alseqs[i].getSequenceAndDeletions(alseqs_string[i],
gapCharacter); // gapped sequence, {start, start col, end.
// endcol}, hidden regions {{start, end, col}})
{
throw new Error(MessageManager.formatMessage(
"error.implementation_error_cigar_seq_no_operations",
- new String[] { Integer.valueOf(i).toString() }));
+ new String[]
+ { Integer.valueOf(i).toString() }));
}
g_seqs[i] = new StringBuffer((String) ((Object[]) gs_regions[i])[0]); // the
// visible
int[] bounds = ((int[]) ((Object[]) gs_regions[i])[1]);
SequenceI ref = alseqs[i].getRefSeq();
seqs[i] = new Sequence(ref.getName(), g_seqs[i].toString(),
- ref.getStart() + alseqs[i].start + bounds[0], ref.getStart()
- + alseqs[i].start + (bounds[2] == 0 ? -1 : bounds[2]));
+ ref.getStart() + alseqs[i].start + bounds[0],
+ ref.getStart() + alseqs[i].start
+ + (bounds[2] == 0 ? -1 : bounds[2]));
seqs[i].setDatasetSequence(ref);
seqs[i].setDescription(ref.getDescription());
}
{
// int start=shifts.shift(segments[i]-1)+1;
// int end=shifts.shift(segments[i]+segments[i+1]-1)-1;
- hidden.hideColumns(segments[i + 1], segments[i + 1]
- + segments[i + 2] - 1);
+ hidden.hideColumns(segments[i + 1],
+ segments[i + 1] + segments[i + 2] - 1);
}
}
return seqs;
*/
int index = -1;
- /** array of sequence features - may not be null for a valid sequence object */
+ /**
+ * array of sequence features - may not be null for a valid sequence object
+ */
public SequenceFeature[] sequenceFeatures;
/**
{
if (name == null)
{
- System.err
- .println("POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor.");
+ System.err.println(
+ "POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor.");
name = "";
}
// Does sequence have the /start-end signature?
{
new Exception(
"Warning: JAL-2046 side effect ? Possible implementation error: overwriting dataset sequence features by setting sequence features on alignment")
- .printStackTrace();
+ .printStackTrace();
}
datasetSequence.setSequenceFeatures(features);
}
}
}
- SequenceFeature[] temp = new SequenceFeature[sequenceFeatures.length + 1];
+ SequenceFeature[] temp = new SequenceFeature[sequenceFeatures.length
+ + 1];
System.arraycopy(sequenceFeatures, 0, temp, 0, sequenceFeatures.length);
temp[sequenceFeatures.length] = sf;
@Override
public AlignmentAnnotation[] getAnnotation()
{
- return annotation == null ? null : annotation
- .toArray(new AlignmentAnnotation[annotation.size()]);
+ return annotation == null ? null
+ : annotation
+ .toArray(new AlignmentAnnotation[annotation.size()]);
}
@Override
{
if (datasetSequence == null)
{
- Sequence dsseq = new Sequence(getName(), AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars, getSequenceAsString()),
+ Sequence dsseq = new Sequence(getName(),
+ AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
+ getSequenceAsString()),
getStart(), getEnd());
datasetSequence = dsseq;
for (int si = 0; si < sfs.length; si++)
{
SequenceFeature sf[] = (mp != null) ? mp.locateFeature(sfs[si])
- : new SequenceFeature[] { new SequenceFeature(sfs[si]) };
+ : new SequenceFeature[]
+ { new SequenceFeature(sfs[si]) };
if (sf != null && sf.length > 0)
{
for (int sfi = 0; sfi < sf.length; sfi++)
}
}
// whilst it looks like it is a primary ref, we also sanity check type
- if (DBRefUtils.getCanonicalName(DBRefSource.PDB).equals(
- DBRefUtils.getCanonicalName(ref.getSource())))
+ if (DBRefUtils.getCanonicalName(DBRefSource.PDB)
+ .equals(DBRefUtils.getCanonicalName(ref.getSource())))
{
// PDB dbrefs imply there should be a PDBEntry associated
// TODO: tighten PDB dbrefs
* @param end
* @param featureGroup
*/
- public SequenceFeature(String type, String desc, String status,
- int begin, int end, String featureGroup)
+ public SequenceFeature(String type, String desc, String status, int begin,
+ int end, String featureGroup)
{
this(type, desc, begin, end, featureGroup);
setStatus(status);
return false;
}
- if (!(type + description + featureGroup + getPhase()).equals(sf.type
- + sf.description + sf.featureGroup + sf.getPhase()))
+ if (!(type + description + featureGroup + getPhase()).equals(
+ sf.type + sf.description + sf.featureGroup + sf.getPhase()))
{
return false;
}
conservation.description = "Conservation for group " + getName()
+ " less than " + consPercGaps + "% gaps";
// preserve width if already set
- int aWidth = (conservation.annotations != null) ? (endRes < conservation.annotations.length ? conservation.annotations.length
- : endRes + 1)
+ int aWidth = (conservation.annotations != null)
+ ? (endRes < conservation.annotations.length
+ ? conservation.annotations.length
+ : endRes + 1)
: endRes + 1;
conservation.annotations = null;
conservation.annotations = new Annotation[aWidth]; // should be alignment
consensus.description = "Percent Identity";
consensusData = cnsns;
// preserve width if already set
- int aWidth = (consensus.annotations != null) ? (endRes < consensus.annotations.length ? consensus.annotations.length
- : endRes + 1)
+ int aWidth = (consensus.annotations != null)
+ ? (endRes < consensus.annotations.length
+ ? consensus.annotations.length
+ : endRes + 1)
: endRes + 1;
consensus.annotations = null;
consensus.annotations = new Annotation[aWidth]; // should be alignment width
ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
for (AlignmentAnnotation ann : getAlignmentAnnotation())
{
- if ((calcId == null || (ann.getCalcId() != null && ann.getCalcId()
- .equals(calcId)))
- && (seq == null || (ann.sequenceRef != null && ann.sequenceRef == seq))
- && (label == null || (ann.label != null && ann.label
- .equals(label))))
+ if ((calcId == null || (ann.getCalcId() != null
+ && ann.getCalcId().equals(calcId)))
+ && (seq == null || (ann.sequenceRef != null
+ && ann.sequenceRef == seq))
+ && (label == null
+ || (ann.label != null && ann.label.equals(label))))
{
aa.add(ann);
}
@Override
public boolean isNucleotide()
{
- if (context != null) {
+ if (context != null)
+ {
return context.isNucleotide();
}
return false;
public class VisibleColsCollection implements AlignmentColsCollectionI
{
int start;
+
int end;
HiddenColumns hidden;
throw new UnsupportedOperationException();
}
}
-
return alignment.getSequenceAtAbsoluteIndex(seq);
}
}
-
* @param alignment
* alignment to work with
*/
- public VisibleRowsIterator(int firstrow, int lastrow, AlignmentI alignment)
+ public VisibleRowsIterator(int firstrow, int lastrow,
+ AlignmentI alignment)
{
al = alignment;
current = firstrow;
throw new UnsupportedOperationException();
}
}
-
return null;
}
dna.setDescription(description);
- DBRefEntry retrievedref = new DBRefEntry(sourceDb,
- getSequenceVersion(), accession);
+ DBRefEntry retrievedref = new DBRefEntry(sourceDb, getSequenceVersion(),
+ accession);
dna.addDBRef(retrievedref);
// add map to indicate the sequence is a valid coordinate frame for the
// dbref
- retrievedref.setMap(new Mapping(null, new int[] { 1, dna.getLength() },
- new int[] { 1, dna.getLength() }, 1, 1));
+ retrievedref
+ .setMap(new Mapping(null, new int[]
+ { 1, dna.getLength() }, new int[] { 1, dna.getLength() }, 1,
+ 1));
/*
* transform EMBL Database refs to canonical form
{
if (sequence == null)
{
- System.err.println("No sequence was returned for ENA accession "
- + accession);
+ System.err.println(
+ "No sequence was returned for ENA accession " + accession);
return null;
}
SequenceI dna = new Sequence(sourceDb + "|" + accession,
* helper to match xrefs in already retrieved sequences
*/
void parseCodingFeature(EmblFeature feature, String sourceDb,
- SequenceI dna, List<SequenceI> peptides, SequenceIdMatcher matcher)
+ SequenceI dna, List<SequenceI> peptides,
+ SequenceIdMatcher matcher)
{
boolean isEmblCdna = sourceDb.equals(DBRefSource.EMBLCDS);
if (qname.equals("translation"))
{
// remove all spaces (precompiled String.replaceAll(" ", ""))
- translation = SPACE_PATTERN.matcher(q.getValues()[0]).replaceAll(
- "");
+ translation = SPACE_PATTERN.matcher(q.getValues()[0])
+ .replaceAll("");
}
else if (qname.equals("protein_id"))
{
codonStart = Integer.parseInt(q.getValues()[0].trim());
} catch (NumberFormatException e)
{
- System.err.println("Invalid codon_start in XML for "
- + accession + ": " + e.getMessage());
+ System.err.println("Invalid codon_start in XML for " + accession
+ + ": " + e.getMessage());
}
}
else if (qname.equals("product"))
product = matcher.findIdMatch(proteinId);
if (product == null)
{
- product = new Sequence(proteinId, translation, 1, translationLength);
- product.setDescription(((proteinName.length() == 0) ? "Protein Product from "
- + sourceDb
+ product = new Sequence(proteinId, translation, 1,
+ translationLength);
+ product.setDescription(((proteinName.length() == 0)
+ ? "Protein Product from " + sourceDb
: proteinName));
peptides.add(product);
matcher.add(product);
* workaround until we handle dna location for CDS sequence
* e.g. location="X53828.1:60..1058" correctly
*/
- System.err
- .println("Implementation Notice: EMBLCDS records not properly supported yet - Making up the CDNA region of this sequence... may be incorrect ("
+ System.err.println(
+ "Implementation Notice: EMBLCDS records not properly supported yet - Making up the CDNA region of this sequence... may be incorrect ("
+ sourceDb + ":" + getAccession() + ")");
- if (translationLength * 3 == (1 - codonStart + dna.getSequence().length))
+ if (translationLength
+ * 3 == (1 - codonStart + dna.getSequence().length))
{
- System.err
- .println("Not allowing for additional stop codon at end of cDNA fragment... !");
+ System.err.println(
+ "Not allowing for additional stop codon at end of cDNA fragment... !");
// this might occur for CDS sequences where no features are marked
exons = new int[] { dna.getStart() + (codonStart - 1),
dna.getEnd() };
- dnaToProteinMapping = new Mapping(product, exons, new int[] { 1,
- translationLength }, 3, 1);
+ dnaToProteinMapping = new Mapping(product, exons,
+ new int[]
+ { 1, translationLength }, 3, 1);
}
- if ((translationLength + 1) * 3 == (1 - codonStart + dna
- .getSequence().length))
+ if ((translationLength + 1)
+ * 3 == (1 - codonStart + dna.getSequence().length))
{
- System.err
- .println("Allowing for additional stop codon at end of cDNA fragment... will probably cause an error in VAMSAs!");
+ System.err.println(
+ "Allowing for additional stop codon at end of cDNA fragment... will probably cause an error in VAMSAs!");
exons = new int[] { dna.getStart() + (codonStart - 1),
dna.getEnd() - 3 };
- dnaToProteinMapping = new Mapping(product, exons, new int[] { 1,
- translationLength }, 3, 1);
+ dnaToProteinMapping = new Mapping(product, exons,
+ new int[]
+ { 1, translationLength }, 3, 1);
}
}
else
else
{
// final product length truncation check
- int[] cdsRanges = adjustForProteinLength(translationLength, exons);
- dnaToProteinMapping = new Mapping(product, cdsRanges, new int[] {
- 1, translationLength }, 3, 1);
+ int[] cdsRanges = adjustForProteinLength(translationLength,
+ exons);
+ dnaToProteinMapping = new Mapping(product, cdsRanges,
+ new int[]
+ { 1, translationLength }, 3, 1);
if (product != null)
{
/*
* make xref with mapping from protein to EMBL dna
*/
DBRefEntry proteinToEmblRef = new DBRefEntry(DBRefSource.EMBL,
- getSequenceVersion(), proteinId, new Mapping(
- dnaToProteinMapping.getMap().getInverse()));
+ getSequenceVersion(), proteinId,
+ new Mapping(dnaToProteinMapping.getMap().getInverse()));
product.addDBRef(proteinToEmblRef);
/*
* make xref from protein to EMBLCDS; we assume here that the
* CDS sequence version is same as dna sequence (?!)
*/
- MapList proteinToCdsMapList = new MapList(new int[] { 1,
- translationLength }, new int[] { 1 + (codonStart - 1),
- (codonStart - 1) + 3 * translationLength }, 1, 3);
+ MapList proteinToCdsMapList = new MapList(
+ new int[]
+ { 1, translationLength },
+ new int[]
+ { 1 + (codonStart - 1),
+ (codonStart - 1) + 3 * translationLength },
+ 1, 3);
DBRefEntry proteinToEmblCdsRef = new DBRefEntry(
DBRefSource.EMBLCDS, getSequenceVersion(), proteinId,
new Mapping(proteinToCdsMapList));
// Add converse mapping reference
if (dnaToProteinMapping != null)
{
- Mapping pmap = new Mapping(dna, dnaToProteinMapping.getMap()
- .getInverse());
+ Mapping pmap = new Mapping(dna,
+ dnaToProteinMapping.getMap().getInverse());
pref = new DBRefEntry(sourceDb, getSequenceVersion(),
this.getAccession());
pref.setMap(pmap);
if (proteinToEmblProteinRef == null)
{
// assuming CDSPROTEIN sequence version = dna version (?!)
- proteinToEmblProteinRef = new DBRefEntry(
- DBRefSource.EMBLCDSProduct, getSequenceVersion(), proteinId);
+ proteinToEmblProteinRef = new DBRefEntry(DBRefSource.EMBLCDSProduct,
+ getSequenceVersion(), proteinId);
}
product.addDBRef(proteinToEmblProteinRef);
&& dnaToProteinMapping.getTo() != null)
{
DBRefEntry dnaToEmblProteinRef = new DBRefEntry(
- DBRefSource.EMBLCDSProduct, getSequenceVersion(), proteinId);
+ DBRefSource.EMBLCDSProduct, getSequenceVersion(),
+ proteinId);
dnaToEmblProteinRef.setMap(dnaToProteinMapping);
dnaToProteinMapping.setMappedFromId(proteinId);
dna.addDBRef(dnaToEmblProteinRef);
sf.setDescription(String.format("Exon %d for protein '%s' EMBLCDS:%s",
exonNumber, proteinName, proteinAccessionId));
sf.setPhase(String.valueOf(codonStart - 1));
- sf.setStrand(exons[exonStartIndex] <= exons[exonStartIndex + 1] ? "+"
- : "-");
+ sf.setStrand(
+ exons[exonStartIndex] <= exons[exonStartIndex + 1] ? "+" : "-");
sf.setValue(FeatureProperties.EXONPOS, exonNumber);
sf.setValue(FeatureProperties.EXONPRODUCT, proteinName);
if (!vals.isEmpty())
return listToArray(ranges);
} catch (ParseException e)
{
- Cache.log.warn(String.format(
- "Not parsing inexact CDS location %s in ENA %s",
- feature.location, this.accession));
+ Cache.log.warn(
+ String.format("Not parsing inexact CDS location %s in ENA %s",
+ feature.location, this.accession));
return new int[] {};
}
}
try
{
// uncomment to DEBUG EMBLFile reading
- if (jalview.bin.Cache.getDefault(jalview.bin.Cache.CASTORLOGLEVEL,
- "debug").equalsIgnoreCase("DEBUG"))
+ if (jalview.bin.Cache
+ .getDefault(jalview.bin.Cache.CASTORLOGLEVEL, "debug")
+ .equalsIgnoreCase("DEBUG"))
{
unmar.setDebug(jalview.bin.Cache.log.isDebugEnabled());
}
* <li>resolves an external identifier by looking up xref-ed gene ids</li>
* <li>fetches the gene sequence</li>
* <li>fetches features on the sequence</li>
- * <li>identifies "transcript" features whose Parent is the requested gene</li>
+ * <li>identifies "transcript" features whose Parent is the requested
+ * gene</li>
* <li>fetches the transcript sequence for each transcript</li>
* <li>makes a mapping from the gene to each transcript</li>
* <li>copies features from gene to transcript sequences</li>
filtered.add(sf);
}
}
- gene.setSequenceFeatures(filtered
- .toArray(new SequenceFeature[filtered.size()]));
+ gene.setSequenceFeatures(
+ filtered.toArray(new SequenceFeature[filtered.size()]));
}
}
* the parent gene sequence, with features
* @return
*/
- SequenceI makeTranscript(SequenceFeature transcriptFeature,
- AlignmentI al, SequenceI gene)
+ SequenceI makeTranscript(SequenceFeature transcriptFeature, AlignmentI al,
+ SequenceI gene)
{
String accId = getTranscriptId(transcriptFeature);
if (accId == null)
mappedFrom.add(new int[] { sf.getBegin(), sf.getEnd() });
}
- Sequence transcript = new Sequence(accId, seqChars, 1, transcriptLength);
+ Sequence transcript = new Sequence(accId, seqChars, 1,
+ transcriptLength);
/*
* Ensembl has gene name as transcript Name
@Override
public boolean isFeatureDisplayed(String type)
{
- return (so.isA(type, SequenceOntologyI.EXON) || so.isA(type,
- SequenceOntologyI.SEQUENCE_VARIANT));
+ return (so.isA(type, SequenceOntologyI.EXON)
+ || so.isA(type, SequenceOntologyI.SEQUENCE_VARIANT));
}
@Override
static
{
domainData = new HashMap<String, EnsemblInfo>();
- domainData.put(ENSEMBL_REST, new EnsemblInfo(ENSEMBL_REST,
- LATEST_ENSEMBL_REST_VERSION));
+ domainData.put(ENSEMBL_REST,
+ new EnsemblInfo(ENSEMBL_REST, LATEST_ENSEMBL_REST_VERSION));
domainData.put(ENSEMBL_GENOMES_REST, new EnsemblInfo(
ENSEMBL_GENOMES_REST, LATEST_ENSEMBLGENOMES_REST_VERSION));
}
{
// note this format works for both ensembl and ensemblgenomes
// info/ping.json works for ensembl only (March 2016)
- URL ping = new URL(getDomain()
- + "/info/ping?content-type=application/json");
+ URL ping = new URL(
+ getDomain() + "/info/ping?content-type=application/json");
/*
* expect {"ping":1} if ok
return pingString != null;
} catch (Throwable t)
{
- System.err.println("Error connecting to " + PING_URL + ": "
- + t.getMessage());
+ System.err.println(
+ "Error connecting to " + PING_URL + ": " + t.getMessage());
} finally
{
if (br != null)
* @return
* @throws IOException
*/
- protected FileParse getSequenceReader(List<String> ids)
- throws IOException
+ protected FileParse getSequenceReader(List<String> ids) throws IOException
{
URL url = getUrl(ids);
// request failed
return null;
}
- FileParse fp = new FileParse(reader, url.toString(), DataSourceType.URL);
+ FileParse fp = new FileParse(reader, url.toString(),
+ DataSourceType.URL);
return fp;
}
* sequence queries, but not for overlap
*/
boolean multipleIds = ids != null && ids.size() > 1;
- connection.setRequestMethod(multipleIds ? HttpMethod.POST
- : HttpMethod.GET);
+ connection.setRequestMethod(
+ multipleIds ? HttpMethod.POST : HttpMethod.GET);
connection.setRequestProperty("Content-Type",
getRequestMimeType(multipleIds));
connection.setRequestProperty("Accept", getResponseMimeType());
+ (1000 * Integer.valueOf(retryDelay));
} catch (NumberFormatException e)
{
- System.err.println("Unexpected value for Retry-After: "
- + retryDelay);
+ System.err
+ .println("Unexpected value for Retry-After: " + retryDelay);
}
}
else
/*
* recheck if Ensembl is up if it was down, or the recheck period has elapsed
*/
- boolean retestAvailability = (now - info.lastAvailableCheckTime) > AVAILABILITY_RETEST_INTERVAL;
+ boolean retestAvailability = (now
+ - info.lastAvailableCheckTime) > AVAILABILITY_RETEST_INTERVAL;
if (!info.restAvailable || retestAvailability)
{
info.restAvailable = checkEnsembl();
/*
* refetch Ensembl versions if the recheck period has elapsed
*/
- boolean refetchVersion = (now - info.lastVersionCheckTime) > VERSION_RETEST_INTERVAL;
+ boolean refetchVersion = (now
+ - info.lastVersionCheckTime) > VERSION_RETEST_INTERVAL;
if (refetchVersion)
{
checkEnsemblRestVersion();
byte[] thepostbody = postBody.toString().getBytes();
connection.setRequestProperty("Content-Length",
Integer.toString(thepostbody.length));
- DataOutputStream wr = new DataOutputStream(connection.getOutputStream());
+ DataOutputStream wr = new DataOutputStream(
+ connection.getOutputStream());
wr.write(thepostbody);
wr.flush();
wr.close();
URL url = null;
try
{
- url = new URL(getDomain()
- + "/info/rest?content-type=application/json");
+ url = new URL(
+ getDomain() + "/info/rest?content-type=application/json");
BufferedReader br = getHttpResponse(url, null);
JSONObject val = (JSONObject) jp.parse(br);
String version = val.get("release").toString();
* if so warn; we don't worry if it is earlier (this indicates Jalview has
* been tested in advance against the next pending REST version)
*/
- boolean laterVersion = StringUtils.compareVersions(version, expected) == 1;
+ boolean laterVersion = StringUtils.compareVersions(version,
+ expected) == 1;
if (laterVersion)
{
- System.err
- .println(String
- .format("EnsemblRestClient expected %s REST version %s but found %s, see %s",
- getDbSource(), expected, version,
- REST_CHANGE_LOG));
+ System.err.println(String.format(
+ "EnsemblRestClient expected %s REST version %s but found %s, see %s",
+ getDbSource(), expected, version, REST_CHANGE_LOG));
}
info.restVersion = version;
} catch (Throwable t)
{
- System.err.println("Error checking Ensembl REST version: "
- + t.getMessage());
+ System.err.println(
+ "Error checking Ensembl REST version: " + t.getMessage());
}
}
URL url = null;
try
{
- url = new URL(getDomain()
- + "/info/data?content-type=application/json");
+ url = new URL(
+ getDomain() + "/info/data?content-type=application/json");
BufferedReader br = getHttpResponse(url, null);
JSONObject val = (JSONObject) jp.parse(br);
JSONArray versions = (JSONArray) val.get("releases");
domainData.get(getDomain()).dataVersion = versions.get(0).toString();
} catch (Throwable t)
{
- System.err.println("Error checking Ensembl data version: "
- + t.getMessage());
+ System.err.println(
+ "Error checking Ensembl data version: " + t.getMessage());
}
}
// danger: accession separator used as a regex here, a string elsewhere
// in this case it is ok (it is just a space), but (e.g.) '\' would not be
- List<String> allIds = Arrays.asList(query
- .split(getAccessionSeparator()));
+ List<String> allIds = Arrays
+ .asList(query.split(getAccessionSeparator()));
AlignmentI alignment = null;
inProgress = true;
}
} catch (IOException e)
{
- System.err.println("Error transferring Ensembl features: "
- + e.getMessage());
+ System.err.println(
+ "Error transferring Ensembl features: " + e.getMessage());
}
}
proteinSeq.createDatasetSequence();
querySeq.createDatasetSequence();
- MapList mapList = AlignmentUtils
- .mapCdsToProtein(querySeq, proteinSeq);
+ MapList mapList = AlignmentUtils.mapCdsToProtein(querySeq,
+ proteinSeq);
if (mapList != null)
{
// clunky: ensure Uniprot xref if we have one is on mapped sequence
getEnsemblDataVersion(), proteinSeq.getName(), map);
querySeq.getDatasetSequence().addDBRef(dbr);
DBRefEntry[] uprots = DBRefUtils.selectRefs(ds.getDBRefs(),
- new String[] { DBRefSource.UNIPROT });
+ new String[]
+ { DBRefSource.UNIPROT });
DBRefEntry[] upxrefs = DBRefUtils.selectRefs(querySeq.getDBRefs(),
- new String[] { DBRefSource.UNIPROT });
+ new String[]
+ { DBRefSource.UNIPROT });
if (uprots != null)
{
for (DBRefEntry up : uprots)
if (upx.size() > 1)
{
- Cache.log
- .warn("Implementation issue - multiple uniprot acc on product sequence.");
+ Cache.log.warn(
+ "Implementation issue - multiple uniprot acc on product sequence.");
}
}
else
* copy exon features to protein, compute peptide variants from dna
* variants and add as features on the protein sequence ta-da
*/
- AlignmentUtils
- .computeProteinFeatures(querySeq, proteinSeq, mapList);
+ AlignmentUtils.computeProteinFeatures(querySeq, proteinSeq,
+ mapList);
}
} catch (Exception e)
{
/*
* and add a reference to itself
*/
- DBRefEntry self = new DBRefEntry(getDbSource(),
- getEnsemblDataVersion(), seq.getName());
+ DBRefEntry self = new DBRefEntry(getDbSource(), getEnsemblDataVersion(),
+ seq.getName());
seq.addDBRef(self);
}
* @throws JalviewException
* @throws IOException
*/
- protected AlignmentI fetchSequences(List<String> ids, AlignmentI alignment)
- throws JalviewException, IOException
+ protected AlignmentI fetchSequences(List<String> ids,
+ AlignmentI alignment) throws JalviewException, IOException
{
if (!isEnsemblAvailable())
{
FastaFile fr = new FastaFile(fp);
if (fr.hasWarningMessage())
{
- System.out.println(String.format(
- "Warning when retrieving %d ids %s\n%s", ids.size(),
- ids.toString(), fr.getWarningMessage()));
+ System.out.println(
+ String.format("Warning when retrieving %d ids %s\n%s",
+ ids.size(), ids.toString(), fr.getWarningMessage()));
}
else if (fr.getSeqs().size() != ids.size())
{
System.out.println(String.format(
- "Only retrieved %d sequences for %d query strings", fr
- .getSeqs().size(), ids.size()));
+ "Only retrieved %d sequences for %d query strings",
+ fr.getSeqs().size(), ids.size()));
}
if (fr.getSeqs().size() == 1 && fr.getSeqs().get(0).getLength() == 0)
if (directionSet && strand != direction)
{
// abort - mix of forward and backward
- System.err.println("Error: forward and backward strand for "
- + accId);
+ System.err.println(
+ "Error: forward and backward strand for " + accId);
return null;
}
direction = strand;
*/
Collections.sort(regions, new RangeComparator(direction == 1));
- List<int[]> to = Arrays.asList(new int[] { start,
- start + mappedLength - 1 });
+ List<int[]> to = Arrays
+ .asList(new int[]
+ { start, start + mappedLength - 1 });
return new MapList(regions, to, 1, 1);
}
* for sequence_variant on reverse strand, have to convert the allele
* values to their complements
*/
- if (!forwardStrand
- && SequenceOntologyFactory.getInstance().isA(sf.getType(),
- SequenceOntologyI.SEQUENCE_VARIANT))
+ if (!forwardStrand && SequenceOntologyFactory.getInstance()
+ .isA(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT))
{
reverseComplementAlleles(copy);
}
* or CCDSnnnnn.nn with at least 3 digits
*/
private static final Regex ACCESSION_REGEX = new Regex(
- "(ENS([A-Z]{3}|)[GTEP]{1}[0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
+ "(ENS([A-Z]{3}|)[GTEP]{1}[0-9]{11}$)" + "|"
+ + "(CCDS[0-9.]{3,}$)");
protected static final String ENSEMBL_GENOMES_REST = "http://rest.ensemblgenomes.org";
* @return
* @throws IOException
*/
- protected String parseSymbolResponse(BufferedReader br)
- throws IOException
+ protected String parseSymbolResponse(BufferedReader br) throws IOException
{
JSONParser jp = new JSONParser();
String result = null;
*/
human(true), mouse(true), s_cerevisiae(true), cow(false), pig(false),
rat(true), celegans(true), sheep(false), horse(false), gorilla(false),
- rabbit(false), gibbon(false), dog(false), orangutan(false),
- xenopus(true), chimpanzee(false), cat(false), zebrafish(true), chicken(
- true), dmelanogaster(true);
+ rabbit(false), gibbon(false), dog(false), orangutan(false), xenopus(true),
+ chimpanzee(false), cat(false), zebrafish(true), chicken(true),
+ dmelanogaster(true);
boolean modelOrganism;
return;
}
- refFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(
- dbLocation, true);
+ refFile = ReferenceSequenceFileFactory
+ .getReferenceSequenceFile(dbLocation, true);
if (refFile == null || refFile.getSequenceDictionary() == null)
{
// refFile = initSequenceDictionaryFor(dbLocation);
ReferenceSequence refSeq;
List<SAMSequenceRecord> ret = new ArrayList<SAMSequenceRecord>();
Set<String> sequenceNames = new HashSet<String>();
- for (int numSequences = 0; (refSeq = refSeqFile.nextSequence()) != null; ++numSequences)
+ for (int numSequences = 0; (refSeq = refSeqFile
+ .nextSequence()) != null; ++numSequences)
{
if (sequenceNames.contains(refSeq.getName()))
{
HiddenColumns hiddenCols)
{
superposeStructures(new AlignmentI[] { alignment },
- new int[] { refStructure },
- new HiddenColumns[] { hiddenCols });
+ new int[]
+ { refStructure }, new HiddenColumns[] { hiddenCols });
}
/**
int refStructure = _refStructure[a];
AlignmentI alignment = _alignment[a];
HiddenColumns hiddenCols = _hiddenCols[a];
- if (a > 0
- && selectioncom.length() > 0
- && !selectioncom.substring(selectioncom.length() - 1).equals(
- "|"))
+ if (a > 0 && selectioncom.length() > 0 && !selectioncom
+ .substring(selectioncom.length() - 1).equals("|"))
{
selectioncom.append("|");
}
// process this alignment
if (refStructure >= files.length)
{
- System.err.println("Invalid reference structure value "
- + refStructure);
+ System.err.println(
+ "Invalid reference structure value " + refStructure);
refStructure = -1;
}
int nmatched = matched.cardinality();
if (nmatched < 4)
{
- return (MessageManager.formatMessage(
-"label.insufficient_residues",
+ return (MessageManager.formatMessage("label.insufficient_residues",
nmatched));
}
command.append(".1} {");
command.append(Integer.toString(1 + refStructure));
// conformation=1 excludes alternate locations for CA (JAL-1757)
- command.append(".1} SUBSET {(*.CA | *.P) and conformation=1} ATOMS ");
+ command.append(
+ ".1} SUBSET {(*.CA | *.P) and conformation=1} ATOMS ");
// for (int s = 0; s < 2; s++)
// {
// System.out.println("Select regions:\n" + selectioncom.toString());
evalStateCommand("select *; cartoons off; backbone; select ("
+ selectioncom.toString() + "); cartoons; ");
- // evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString());
+ // evalStateCommand("select *; backbone; select "+selcom.toString()+";
+ // cartoons; center "+selcom.toString());
}
return null;
}
@Override
- public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
+ public float[][][] functionXYZ(String functionName, int nx, int ny,
+ int nz)
{
// TODO Auto-generated method stub
return null;
} catch (AccessControlException x)
{
// usually not allowed to do this in applet
- System.err
- .println("jmolBinding: Using local file string from Jmol: "
- + m);
+ System.err.println(
+ "jmolBinding: Using local file string from Jmol: " + m);
}
if (filePath.indexOf("/file:") != -1)
{
} catch (AccessControlException x)
{
// usually not allowed to do this in applet, so keep raw handle
- // System.err.println("jmolBinding: Using local file string from Jmol: "+m);
+ // System.err.println("jmolBinding: Using local file string from
+ // Jmol: "+m);
}
}
return modelFileNames;
}
+
/**
* map from string to applet
*/
return null;
}
-
-
// ///////////////////////////////
// JmolStatusListener
// handle insertion codes
if (alocsep != -1)
{
- pdbResNum = Integer.parseInt(strInfo.substring(
- strInfo.indexOf("]") + 1, alocsep));
+ pdbResNum = Integer.parseInt(
+ strInfo.substring(strInfo.indexOf("]") + 1, alocsep));
}
else
{
- pdbResNum = Integer.parseInt(strInfo.substring(
- strInfo.indexOf("]") + 1, chainSeparator));
+ pdbResNum = Integer.parseInt(
+ strInfo.substring(strInfo.indexOf("]") + 1, chainSeparator));
}
String chainId;
{
chainSeparator1 = strInfo.indexOf(".", mdlSep);
}
- String mdlId = (chainSeparator1 > -1) ? strInfo.substring(mdlSep + 1,
- chainSeparator1) : strInfo.substring(mdlSep + 1);
+ String mdlId = (chainSeparator1 > -1)
+ ? strInfo.substring(mdlSep + 1, chainSeparator1)
+ : strInfo.substring(mdlSep + 1);
try
{
// recover PDB filename for the model hovered over.
- int _mp = _modelFileNameMap.length - 1, mnumber = new Integer(mdlId)
- .intValue() - 1;
+ int _mp = _modelFileNameMap.length - 1,
+ mnumber = new Integer(mdlId).intValue() - 1;
while (mnumber < _modelFileNameMap[_mp])
{
_mp--;
* } }
*/
- public void notifyAtomPicked(int atomIndex, String strInfo, String strData)
+ public void notifyAtomPicked(int atomIndex, String strInfo,
+ String strData)
{
/**
* this implements the toggle label behaviour copied from the original
sendConsoleEcho((String) data[1]);
break;
case MESSAGE:
- sendConsoleMessage((data == null) ? ((String) null)
- : (String) data[1]);
+ sendConsoleMessage(
+ (data == null) ? ((String) null) : (String) data[1]);
break;
case ERROR:
// System.err.println("Ignoring error callback.");
case CLICK:
default:
- System.err.println("Unhandled callback " + type + " "
- + data[1].toString());
+ System.err.println(
+ "Unhandled callback " + type + " " + data[1].toString());
break;
}
} catch (Exception e)
// calculate essential attributes for the pdb data imported inline.
// prolly need to resolve modelnumber properly - for now just use our
// 'best guess'
- pdbfile = viewer.getData("" + (1 + _modelFileNameMap[modelnum])
- + ".0", "PDB");
+ pdbfile = viewer.getData(
+ "" + (1 + _modelFileNameMap[modelnum]) + ".0", "PDB");
}
// search pdbentries and sequences to find correct pdbentry for this
// model
// add an entry for every chain in the model
for (int i = 0; i < pdb.getChains().size(); i++)
{
- String chid = new String(pdb.getId() + ":"
- + pdb.getChains().elementAt(i).id);
+ String chid = new String(
+ pdb.getId() + ":" + pdb.getChains().elementAt(i).id);
chainFile.put(chid, fileName);
chainNames.add(chid);
}
// }
if (!isLoadingFromArchive())
{
- viewer.evalStringQuiet("model *; select backbone;restrict;cartoon;wireframe off;spacefill off");
+ viewer.evalStringQuiet(
+ "model *; select backbone;restrict;cartoon;wireframe off;spacefill off");
}
// register ourselves as a listener and notify the gui that it needs to
// update itself.
false);
for (String resName : residueSet)
{
- char res = resName.length() == 3 ? ResidueProperties
- .getSingleCharacterCode(resName) : resName.charAt(0);
+ char res = resName.length() == 3
+ ? ResidueProperties.getSingleCharacterCode(resName)
+ : resName.charAt(0);
Color col = cs.findColour(res, 0, null, null, 0f);
command.append("select " + resName + ";color[" + col.getRed() + ","
+ col.getGreen() + "," + col.getBlue() + "];");
commandOptions = "";
}
viewer = (Viewer) JmolViewer.allocateViewer(renderPanel,
- (jmolfileio ? new SmarterJmolAdapter() : null), htmlName
- + ((Object) this).toString(), documentBase, codeBase,
+ (jmolfileio ? new SmarterJmolAdapter() : null),
+ htmlName + ((Object) this).toString(), documentBase, codeBase,
commandOptions, this);
viewer.setJmolStatusListener(this); // extends JmolCallbackListener
col = Color.GRAY;
}
- String newSelcom = (mapping[m].getChain() != " " ? ":"
- + mapping[m].getChain() : "")
- + "/"
- + (pdbfnum + 1)
- + ".1"
- + ";color["
- + col.getRed()
- + ","
- + col.getGreen()
- + ","
+ String newSelcom = (mapping[m].getChain() != " "
+ ? ":" + mapping[m].getChain()
+ : "") + "/" + (pdbfnum + 1) + ".1" + ";color["
+ + col.getRed() + "," + col.getGreen() + ","
+ col.getBlue() + "]";
- if (command.length() > newSelcom.length()
- && command.substring(
- command.length() - newSelcom.length())
- .equals(newSelcom))
+ if (command.length() > newSelcom.length() && command
+ .substring(command.length() - newSelcom.length())
+ .equals(newSelcom))
{
command = JmolCommands.condenseCommand(command, pos);
continue;
// }
// ;
// instead, we distinguish .cif from non-.cif by filename
- setStructureFileType(getDataName().toLowerCase().endsWith(".cif") ? PDBEntry.Type.MMCIF
- .toString() : "PDB");
+ setStructureFileType(getDataName().toLowerCase().endsWith(".cif")
+ ? PDBEntry.Type.MMCIF.toString()
+ : "PDB");
transformJmolModelToJalview(jmolModel.ms);
}
{
throw new Error(MessageManager.formatMessage(
"error.jmol_version_not_compatible_with_jalview_version",
- new String[] { JmolViewer.getJmolVersion() }), x);
+ new String[]
+ { JmolViewer.getJmolVersion() }), x);
}
}
return viewer;
}
} catch (OutOfMemoryError er)
{
- System.out
- .println("OUT OF MEMORY LOADING TRANSFORMING JMOL MODEL TO JALVIEW MODEL");
- throw new IOException(
- MessageManager
- .getString("exception.outofmemory_loading_mmcif_file"));
+ System.out.println(
+ "OUT OF MEMORY LOADING TRANSFORMING JMOL MODEL TO JALVIEW MODEL");
+ throw new IOException(MessageManager
+ .getString("exception.outofmemory_loading_mmcif_file"));
}
}
curAtom.number = atom.getAtomNumber();
curAtom.resName = atom.getGroup3(true);
curAtom.resNumber = atom.getResno();
- curAtom.occupancy = ms.occupancies != null ? ms.occupancies[atom
- .getIndex()] : Float.valueOf(atom.getOccupancy100());
+ curAtom.occupancy = ms.occupancies != null
+ ? ms.occupancies[atom.getIndex()]
+ : Float.valueOf(atom.getOccupancy100());
String fmt = new Format("%4i").form(curAtom.resNumber);
curAtom.resNumIns = (fmt + curAtom.insCode);
curAtom.tfactor = atom.getBfactor100() / 100f;
HashMap<String, org.jmol.modelset.Atom> chainTerMap)
{
// System.out.println("Atom: " + curAtom.getAtomNumber()
- // + " Last atom index " + curAtom.group.lastAtomIndex);
+ // + " Last atom index " + curAtom.group.lastAtomIndex);
if (chainTerMap == null || prevAtom == null)
{
return true;
{
return false;
}
- if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
+ if ((curAtom.getResno()
+ - chainTerMap.get(curAtomChId).getResno()) < 5)
{
chainTerMap.put(curAtomChId, curAtom);
return true;
{
return false;
}
- if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
+ if ((curAtom.getResno()
+ - chainTerMap.get(curAtomChId).getResno()) < 5)
{
chainTerMap.put(curAtomChId, curAtom);
return true;
return false;
}
// HETATM with resNum jump > 2
- return !(curAtom.isHetero() && ((curAtom.getResno() - prevAtom
- .getResno()) > 2));
+ return !(curAtom.isHetero()
+ && ((curAtom.getResno() - prevAtom.getResno()) > 2));
}
private void createAnnotation(SequenceI sequence, PDBChain chain,
* @param secstr
* @param secstrcode
*/
- protected void setSecondaryStructure(STR proteinStructureSubType,
- int pos, char[] secstr, char[] secstrcode)
+ protected void setSecondaryStructure(STR proteinStructureSubType, int pos,
+ char[] secstr, char[] secstrcode)
{
switch (proteinStructureSubType)
{
@Override
public void notifyCallback(CBK cbType, Object[] data)
{
- String strInfo = (data == null || data[1] == null ? null : data[1]
- .toString());
+ String strInfo = (data == null || data[1] == null ? null
+ : data[1].toString());
switch (cbType)
{
case ECHO:
* Not implemented - returns null
*/
@Override
- public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
+ public float[][][] functionXYZ(String functionName, int nx, int ny,
+ int nz)
{
return null;
}
return predictSecondaryStructure;
}
- public void setPredictSecondaryStructure(boolean predictSecondaryStructure)
+ public void setPredictSecondaryStructure(
+ boolean predictSecondaryStructure)
{
this.predictSecondaryStructure = predictSecondaryStructure;
}
}
@Override
- public boolean startObjectEntry(String key) throws ParseException,
- IOException
+ public boolean startObjectEntry(String key)
+ throws ParseException, IOException
{
// TODO Auto-generated method stub
return false;
}
@Override
- public boolean primitive(Object value) throws ParseException,
- IOException
+ public boolean primitive(Object value)
+ throws ParseException, IOException
{
// TODO Auto-generated method stub
return false;
// return processJsonResponseFor(HttpClientUtils.doHttpUrlPost(twoDtoolsURL,
// vals));
ArrayList<Reader> readers = new ArrayList<Reader>();
- final BufferedReader postResponse = HttpClientUtils.doHttpUrlPost(
- twoDtoolsURL, vals, 0, 0);
+ final BufferedReader postResponse = HttpClientUtils
+ .doHttpUrlPost(twoDtoolsURL, vals, 0, 0);
readers.add(postResponse);
return readers.iterator();
;
if (sval == null)
{
- System.err
- .println("DEVELOPER WARNING: Annotate3d didn't return a '2D' tag in its response. Consider checking output of server. Response was :"
+ System.err.println(
+ "DEVELOPER WARNING: Annotate3d didn't return a '2D' tag in its response. Consider checking output of server. Response was :"
+ val.toString());
sval = "";
}
- return new StringReader(
- (sval instanceof JSONObject) ? ((JSONObject) sval)
- .toString() : sval.toString());
+ return new StringReader((sval instanceof JSONObject)
+ ? ((JSONObject) sval).toString()
+ : sval.toString());
}
};
} catch (Exception foo)
{
- throw new Exception(
- MessageManager
- .getString("exception.couldnt_parse_responde_from_annotated3d_server"),
+ throw new Exception(MessageManager.getString(
+ "exception.couldnt_parse_responde_from_annotated3d_server"),
foo);
}
* </ul>
*
* <pre>
- * @see http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec.html
+ * @see http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec.html
* </pre>
*/
public class AtomSpecModel
// final colour range
if (lastColour != null)
{
- addColourRange(colourMap, lastColour, pdbfnum, startPos, lastPos,
- lastChain);
+ addColourRange(colourMap, lastColour, pdbfnum, startPos,
+ lastPos, lastChain);
}
// break;
}
* @return
*/
public static StructureMappingcommandSet getSetAttributeCommandsForFeatures(
- StructureSelectionManager ssm, String[] files,
- SequenceI[][] seqs, AlignmentViewPanel viewPanel)
+ StructureSelectionManager ssm, String[] files, SequenceI[][] seqs,
+ AlignmentViewPanel viewPanel)
{
Map<String, Map<Object, AtomSpecModel>> featureMap = buildFeaturesMap(
ssm, files, seqs, viewPanel);
* @return
*/
protected static Map<String, Map<Object, AtomSpecModel>> buildFeaturesMap(
- StructureSelectionManager ssm, String[] files,
- SequenceI[][] seqs, AlignmentViewPanel viewPanel)
+ StructureSelectionManager ssm, String[] files, SequenceI[][] seqs,
+ AlignmentViewPanel viewPanel)
{
Map<String, Map<Object, AtomSpecModel>> theMap = new LinkedHashMap<String, Map<Object, AtomSpecModel>>();
}
for (int[] range : mappedRanges)
{
- addColourRange(featureValues, value, modelNumber, range[0], range[1],
- mapping.getChain());
+ addColourRange(featureValues, value, modelNumber, range[0],
+ range[1], mapping.getChain());
}
}
}
* to an underscore.
*
* @param featureType
- * @return <pre>
- * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html
- * </pre>
+ * @return
+ *
+ * <pre>
+ * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html
+ * </pre>
*/
protected static String makeAttributeName(String featureType)
{
* <li>Start the ChimeraListener, get the URL it is listening on</li>
* <li>The first listener started will start the singleton HttpServer</li>
* <li>Send a 'listen' command to Chimera with the URL of the listener</li>
- * <li>When Jalview's Chimera window is closed, shut down the ChimeraListener</li>
+ * <li>When Jalview's Chimera window is closed, shut down the
+ * ChimeraListener</li>
* <li>Multiple linked Chimera instances will each have a separate listener (but
* share one Http server)</li>
* </ul>
* @author gmcarstairs
*
*/
-public class ChimeraListener extends AbstractRequestHandler implements
- SelectionSource
+public class ChimeraListener extends AbstractRequestHandler
+ implements SelectionSource
{
/*
* Chimera notification parameter name
* @throws BindException
* if no free port can be assigned
*/
- public ChimeraListener(JalviewChimeraBinding binding)
- throws BindException
+ public ChimeraListener(JalviewChimeraBinding binding) throws BindException
{
myChimeraId = chimeraId++;
this.chimeraBinding = binding;
private List<String> chainNames = new ArrayList<String>();
private Hashtable<String, String> chainFile = new Hashtable<String, String>();
-
+
/*
* Object through which we talk to Chimera
*/
* @param protocol
*/
public JalviewChimeraBinding(StructureSelectionManager ssm,
- PDBEntry[] pdbentry, SequenceI[][] sequenceIs, DataSourceType protocol)
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
+ DataSourceType protocol)
{
super(ssm, pdbentry, sequenceIs, protocol);
viewer = new ChimeraManager(new StructureManager(true));
viewer.startListening(chimeraListener.getUri());
} catch (BindException e)
{
- System.err.println("Failed to start Chimera listener: "
- + e.getMessage());
+ System.err.println(
+ "Failed to start Chimera listener: " + e.getMessage());
}
}
for (String chain : toshow)
{
int modelNumber = getModelNoForChain(chain);
- String showChainCmd = modelNumber == -1 ? "" : modelNumber + ":."
- + chain.split(":")[1];
+ String showChainCmd = modelNumber == -1 ? ""
+ : modelNumber + ":." + chain.split(":")[1];
if (!first)
{
cmd.append(",");
if (debug)
{
System.out.println("Select regions:\n" + selectioncom.toString());
- System.out.println("Superimpose command(s):\n"
- + command.toString());
+ System.out.println(
+ "Superimpose command(s):\n" + command.toString());
}
allComs.append("~display all; chain @CA|P; ribbon ")
.append(selectioncom.toString())
return true;
}
- boolean launched = viewer.launchChimera(StructureManager
- .getChimeraPaths());
+ boolean launched = viewer
+ .launchChimera(StructureManager.getChimeraPaths());
if (launched)
{
startChimeraProcessMonitor();
*/
private int _modelFileNameMap[];
-
// ////////////////////////////////
// /StructureListener
@Override
return new String[0];
}
- return chimeraMaps.keySet().toArray(
- modelFileNames = new String[chimeraMaps.size()]);
+ return chimeraMaps.keySet()
+ .toArray(modelFileNames = new String[chimeraMaps.size()]);
}
/**
* Parse model number, residue and chain for each selected position,
* formatted as #0:123.A or #1.2:87.B (#model.submodel:residue.chain)
*/
- List<AtomSpec> atomSpecs = convertStructureResiduesToAlignment(selection);
+ List<AtomSpec> atomSpecs = convertStructureResiduesToAlignment(
+ selection);
/*
* Broadcast the selection (which may be empty, if the user just cleared all
false);
for (String resName : residueSet)
{
- char res = resName.length() == 3 ? ResidueProperties
- .getSingleCharacterCode(resName) : resName.charAt(0);
+ char res = resName.length() == 3
+ ? ResidueProperties.getSingleCharacterCode(resName)
+ : resName.charAt(0);
Color col = cs.findColour(res, 0, null, null, 0f);
command.append("color " + col.getRed() / normalise + ","
- + col.getGreen() / normalise + "," + col.getBlue()
- / normalise + " ::" + resName + ";");
+ + col.getGreen() / normalise + "," + col.getBlue() / normalise
+ + " ::" + resName + ";");
}
sendAsynchronousCommand(command.toString(), COLOURING_CHIMERA);
/**
* Send the Chimera 'background solid <color>" command.
*
- * @see https
+ * @see https
* ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/background
* .html
* @param col
viewerCommandHistory(false);
double normalise = 255D;
final String command = "background solid " + col.getRed() / normalise
- + "," + col.getGreen() / normalise + "," + col.getBlue()
- / normalise + ";";
+ + "," + col.getGreen() / normalise + ","
+ + col.getBlue() / normalise + ";";
viewer.sendChimeraCommand(command, false);
viewerCommandHistory(true);
}
sendAsynchronousCommand("open cmd:" + path, null);
} catch (IOException e)
{
- System.err
- .println("Sending commands to Chimera via file failed with "
- + e.getMessage());
+ System.err.println("Sending commands to Chimera via file failed with "
+ + e.getMessage());
}
}
return CHIMERA_FEATURE_GROUP;
}
-
public Hashtable<String, String> getChainFile()
{
return chainFile;
try
{
String zipFile = ontologyFile + ".zip";
- InputStream inStream = this.getClass().getResourceAsStream(
- "/" + zipFile);
+ InputStream inStream = this.getClass()
+ .getResourceAsStream("/" + zipFile);
zipStream = new ZipInputStream(new BufferedInputStream(inStream));
ZipEntry entry;
while ((entry = zipStream.getNextEntry()) != null)
* @throws ParseException
* @throws IOException
*/
- protected void loadOboFile(InputStream is) throws ParseException,
- IOException
+ protected void loadOboFile(InputStream is)
+ throws ParseException, IOException
{
BufferedReader oboFile = new BufferedReader(new InputStreamReader(is));
OboParser parser = new OboParser();
import java.awt.event.ComponentListener;
-public abstract class JalviewVarnaBinding extends
- SequenceStructureBindingModel implements StructureListener,
+public abstract class JalviewVarnaBinding
+ extends SequenceStructureBindingModel implements StructureListener,
ComponentListener, StructureSelectionManagerProvider
{
public static String[] getColourBySequenceCommand(
StructureSelectionManager ssm, String[] files,
SequenceI[][] sequence, SequenceRenderer sr,
- FeatureColourFinder finder,
- AlignmentI alignment)
+ FeatureColourFinder finder, AlignmentI alignment)
{
ArrayList<String> str = new ArrayList<String>();
StringBuffer command = new StringBuffer();
Color col = sr.getResidueColour(sequence[pdbfnum][s], r,
finder);
- String newSelcom = (mapping[m].getChain() != " " ? ":"
- + mapping[m].getChain() : "")
- + "/"
- + (pdbfnum + 1)
- + ".1"
- + ";color["
- + col.getRed()
- + ","
- + col.getGreen()
- + ","
+ String newSelcom = (mapping[m].getChain() != " "
+ ? ":" + mapping[m].getChain()
+ : "") + "/" + (pdbfnum + 1) + ".1" + ";color["
+ + col.getRed() + "," + col.getGreen() + ","
+ col.getBlue() + "]";
- if (command.length() > newSelcom.length()
- && command.substring(
- command.length() - newSelcom.length())
- .equals(newSelcom))
+ if (command.length() > newSelcom.length() && command
+ .substring(command.length() - newSelcom.length())
+ .equals(newSelcom))
{
command = VarnaCommands.condenseCommand(command, pos);
continue;
/**
* The class to handle the formatting of the double values for JTable cells.
*/
-public class DecimalFormatTableCellRenderer extends
- DefaultTableCellRenderer
+public class DecimalFormatTableCellRenderer extends DefaultTableCellRenderer
{
private DecimalFormat formatter;
{
significantFigureBuilder.append("0");
}
- formatter = new DecimalFormat(fractionFormater
- + significantFigureBuilder.toString());
+ formatter = new DecimalFormat(
+ fractionFormater + significantFigureBuilder.toString());
}
else
{
}
@Override
- public Component getTableCellRendererComponent(JTable table,
- Object value, boolean isSelected, boolean hasFocus, int row,
- int column)
+ public Component getTableCellRendererComponent(JTable table, Object value,
+ boolean isSelected, boolean hasFocus, int row, int column)
{
if (value == null)
{
switch (source)
{
case SEARCH_SUMMARY:
- data[x++] = new Object[] {
- ftsRestClient.getAllDefaultDisplayedFTSDataColumns().contains(
- field), field.getName(), field.getGroup() };
+ data[x++] = new Object[] { ftsRestClient
+ .getAllDefaultDisplayedFTSDataColumns().contains(field),
+ field.getName(), field.getGroup() };
break;
case STRUCTURE_CHOOSER:
data[x++] = new Object[] { structSummaryColumns.contains(field),
break;
case PREFERENCES:
data[x++] = new Object[] {
- field.getName(),
- ftsRestClient.getAllDefaultDisplayedFTSDataColumns().contains(
- field), structSummaryColumns.contains(field) };
+ field.getName(), ftsRestClient
+ .getAllDefaultDisplayedFTSDataColumns().contains(field),
+ structSummaryColumns.contains(field) };
break;
default:
break;
{
primaryKeyColumnCode = lineData[1];
}
- if (lineData[0]
- .equalsIgnoreCase("_data_column.default_response_page_size"))
+ if (lineData[0].equalsIgnoreCase(
+ "_data_column.default_response_page_size"))
{
defaultResponsePageSize = Integer.valueOf(lineData[1]);
}
@Override
public String getAltCode()
{
- return lineData[1].split("\\|").length > 1 ? lineData[1]
- .split("\\|")[1] : getCode();
+ return lineData[1].split("\\|").length > 1
+ ? lineData[1].split("\\|")[1]
+ : getCode();
}
@Override
}
try
{
- this.primaryKeyColumn = getDataColumnByNameOrCode(primaryKeyColumnCode);
+ this.primaryKeyColumn = getDataColumnByNameOrCode(
+ primaryKeyColumnCode);
} catch (Exception e)
{
e.printStackTrace();
return column;
}
}
- throw new Exception("Couldn't find data column with name : "
- + nameOrCode);
+ throw new Exception(
+ "Couldn't find data column with name : " + nameOrCode);
}
@Override
private boolean allowEmptySequence;
- private boolean allowUnpublishedEntries = Cache.getDefault(
- "ALLOW_UNPUBLISHED_PDB_QUERYING", false);
+ private boolean allowUnpublishedEntries = Cache
+ .getDefault("ALLOW_UNPUBLISHED_PDB_QUERYING", false);
private boolean facet;
return fieldToSortBy;
}
- public void setFieldToSortBy(String fieldToSortBy, boolean isSortAscending)
+ public void setFieldToSortBy(String fieldToSortBy,
+ boolean isSortAscending)
{
this.fieldToSortBy = fieldToSortBy;
this.isSortAscending = isSortAscending;
public static DefaultTableModel getTableModel(FTSRestRequest request,
Collection<FTSData> summariesList)
{
- final FTSDataColumnI[] cols = request.getWantedFields().toArray(
- new FTSDataColumnI[0]);
+ final FTSDataColumnI[] cols = request.getWantedFields()
+ .toArray(new FTSDataColumnI[0]);
final int colOffset = request.getAssociatedSequence() == null ? 0 : 1;
DefaultTableModel tableModel = new DefaultTableModel()
{
{
try
{
- tbl_summary.getColumn(wantedField.getName()).setMinWidth(
- wantedField.getMinWidth());
- tbl_summary.getColumn(wantedField.getName()).setMaxWidth(
- wantedField.getMaxWidth());
- int prefedWidth = columnPrefs.get(wantedField.getName()) == null ? wantedField
- .getPreferredWidth() : columnPrefs.get(wantedField
- .getName());
- tbl_summary.getColumn(wantedField.getName()).setPreferredWidth(
- prefedWidth);
+ tbl_summary.getColumn(wantedField.getName())
+ .setMinWidth(wantedField.getMinWidth());
+ tbl_summary.getColumn(wantedField.getName())
+ .setMaxWidth(wantedField.getMaxWidth());
+ int prefedWidth = columnPrefs.get(wantedField.getName()) == null
+ ? wantedField.getPreferredWidth()
+ : columnPrefs.get(wantedField.getName());
+ tbl_summary.getColumn(wantedField.getName())
+ .setPreferredWidth(prefedWidth);
} catch (Exception e)
{
e.printStackTrace();
if (wantedField.getDataType().getDataTypeClass() == Double.class)
{
DecimalFormatTableCellRenderer dfr = new DecimalFormatTableCellRenderer(
- wantedField.getDataType().isFormtted(), wantedField
- .getDataType().getSignificantFigures());
+ wantedField.getDataType().isFormtted(),
+ wantedField.getDataType().getSignificantFigures());
tbl_summary.getColumn(wantedField.getName()).setCellRenderer(dfr);
}
- else if (wantedField.getDataType().getDataTypeClass() == Integer.class)
+ else if (wantedField.getDataType()
+ .getDataTypeClass() == Integer.class)
{
DecimalFormatTableCellRenderer dfr = new DecimalFormatTableCellRenderer(
- wantedField.getDataType().isFormtted(), wantedField
- .getDataType().getSignificantFigures());
+ wantedField.getDataType().isFormtted(),
+ wantedField.getDataType().getSignificantFigures());
tbl_summary.getColumn(wantedField.getName()).setCellRenderer(dfr);
}
}
protected StringBuilder errorWarning = new StringBuilder();
- protected ImageIcon warningImage = new ImageIcon(getClass().getResource(
- "/images/warning.gif"));
+ protected ImageIcon warningImage = new ImageIcon(
+ getClass().getResource("/images/warning.gif"));
- protected ImageIcon loadingImage = new ImageIcon(getClass().getResource(
- "/images/loading.gif"));
+ protected ImageIcon loadingImage = new ImageIcon(
+ getClass().getResource("/images/loading.gif"));
- protected ImageIcon balnkPlaceholderImage = new ImageIcon(getClass()
- .getResource("/images/blank_16x16_placeholder.png"));
+ protected ImageIcon balnkPlaceholderImage = new ImageIcon(
+ getClass().getResource("/images/blank_16x16_placeholder.png"));
protected JLabel lbl_warning = new JLabel(warningImage);
e.printStackTrace();
}
toolTipText = (toolTipText == null ? null
- : (toolTipText.length() > 500 ? JvSwingUtils.wrapTooltip(
- true, toolTipText.subSequence(0, 500) + "...")
+ : (toolTipText.length() > 500
+ ? JvSwingUtils.wrapTooltip(true,
+ toolTipText.subSequence(0, 500) + "...")
: JvSwingUtils.wrapTooltip(true, toolTipText)));
return toolTipText;
}
});
btn_next_page.setEnabled(false);
- btn_next_page.setToolTipText(MessageManager
- .getString("label.next_page_tooltip"));
+ btn_next_page.setToolTipText(
+ MessageManager.getString("label.next_page_tooltip"));
btn_next_page.setFont(new java.awt.Font("Verdana", 0, 12));
btn_next_page.setText(MessageManager.getString("action.next_page"));
btn_next_page.addActionListener(new java.awt.event.ActionListener()
});
btn_prev_page.setEnabled(false);
- btn_prev_page.setToolTipText(MessageManager
- .getString("label.prev_page_tooltip"));
+ btn_prev_page.setToolTipText(
+ MessageManager.getString("label.prev_page_tooltip"));
btn_prev_page.setFont(new java.awt.Font("Verdana", 0, 12));
btn_prev_page.setText(MessageManager.getString("action.prev_page"));
btn_prev_page.addActionListener(new java.awt.event.ActionListener()
if (e.getStateChange() == ItemEvent.SELECTED)
{
String tooltipText;
- if ("all".equalsIgnoreCase(getCmbSearchTarget().getSelectedItem()
- .toString()))
+ if ("all".equalsIgnoreCase(
+ getCmbSearchTarget().getSelectedItem().toString()))
{
tooltipText = MessageManager.getString("label.search_all");
}
- else if ("pdb id".equalsIgnoreCase(getCmbSearchTarget()
- .getSelectedItem().toString()))
+ else if ("pdb id".equalsIgnoreCase(
+ getCmbSearchTarget().getSelectedItem().toString()))
{
tooltipText = MessageManager
.getString("label.separate_multiple_accession_ids");
else
{
tooltipText = MessageManager.formatMessage(
- "label.separate_multiple_query_values",
- new Object[] { getCmbSearchTarget().getSelectedItem()
- .toString() });
+ "label.separate_multiple_query_values", new Object[]
+ { getCmbSearchTarget().getSelectedItem().toString() });
}
- txt_search.setToolTipText(JvSwingUtils.wrapTooltip(true,
- tooltipText));
+ txt_search.setToolTipText(
+ JvSwingUtils.wrapTooltip(true, tooltipText));
searchAction(true);
}
}
});
-
txt_search.setFont(new java.awt.Font("Verdana", 0, 12));
txt_search.getEditor().getEditorComponent()
.addKeyListener(new KeyAdapter()
- {
- @Override
- public void keyPressed(KeyEvent e)
- {
- if (e.getKeyCode() == KeyEvent.VK_ENTER)
- {
- if (getTypedText() == null || getTypedText().isEmpty())
- {
- return;
- }
- String primaryKeyName = getFTSRestClient().getPrimaryKeyColumn()
- .getName();
- if (primaryKeyName.equalsIgnoreCase(getCmbSearchTarget()
- .getSelectedItem().toString()))
- {
- transferToSequenceFetcher(getTypedText());
- }
- }
- }
- });
+ {
+ @Override
+ public void keyPressed(KeyEvent e)
+ {
+ if (e.getKeyCode() == KeyEvent.VK_ENTER)
+ {
+ if (getTypedText() == null || getTypedText().isEmpty())
+ {
+ return;
+ }
+ String primaryKeyName = getFTSRestClient()
+ .getPrimaryKeyColumn().getName();
+ if (primaryKeyName.equalsIgnoreCase(getCmbSearchTarget()
+ .getSelectedItem().toString()))
+ {
+ transferToSequenceFetcher(getTypedText());
+ }
+ }
+ }
+ });
final DeferredTextInputListener listener = new DeferredTextInputListener(
1500, new ActionListener()
{
txt_search.setEnabled(false);
cmb_searchTarget.setEnabled(false);
previousWantedFields = getFTSRestClient()
- .getAllDefaultDisplayedFTSDataColumns().toArray(
- new Object[0]);
+ .getAllDefaultDisplayedFTSDataColumns()
+ .toArray(new Object[0]);
}
if (sourceTabbedPane.getTitleAt(index).equals(searchTabTitle))
{
mainFrame.setVisible(true);
mainFrame.setContentPane(this);
mainFrame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
- mainFrame
- .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+ mainFrame.addInternalFrameListener(
+ new javax.swing.event.InternalFrameAdapter()
{
@Override
public void internalFrameClosing(InternalFrameEvent e)
{
lbl_loading.setVisible(false);
lbl_blank.setVisible(false);
- lbl_warning.setToolTipText(JvSwingUtils.wrapTooltip(true,
- errorWarning.toString()));
+ lbl_warning.setToolTipText(
+ JvSwingUtils.wrapTooltip(true, errorWarning.toString()));
lbl_warning.setVisible(true);
}
}
int totalRows = resultTable.getRowCount();
try
{
- primaryKeyColIndex = getFTSRestClient().getPrimaryKeyColumIndex(
- wantedFields, false);
+ primaryKeyColIndex = getFTSRestClient()
+ .getPrimaryKeyColumIndex(wantedFields, false);
} catch (Exception e)
{
e.printStackTrace();
int primaryKeyColIndex = 0;
try
{
- primaryKeyColIndex = getFTSRestClient().getPrimaryKeyColumIndex(
- wantedFields, false);
+ primaryKeyColIndex = getFTSRestClient()
+ .getPrimaryKeyColumIndex(wantedFields, false);
} catch (Exception e)
{
e.printStackTrace();
mainFrame.setTitle(getFTSFrameTitle());
}
-
}
private static String defaultFTSFrameTitle = MessageManager
.getString("label.pdb_sequence_fetcher");
-
private static Map<String, Integer> tempUserPrefs = new HashMap<String, Integer>();
private static final String PDB_FTS_CACHE_KEY = "CACHE.PDB_FTS";
super();
pageLimit = PDBFTSRestClient.getInstance().getDefaultResponsePageSize();
this.seqFetcher = seqFetcher;
- this.progressIndicator = (seqFetcher == null) ? null : seqFetcher
- .getProgressIndicator();
+ this.progressIndicator = (seqFetcher == null) ? null
+ : seqFetcher.getProgressIndicator();
}
@Override
if (resultList.getSearchSummary() != null
&& resultList.getSearchSummary().size() > 0)
{
- getResultTable().setModel(
- FTSRestResponse.getTableModel(request,
- resultList.getSearchSummary()));
+ getResultTable().setModel(FTSRestResponse.getTableModel(request,
+ resultList.getSearchSummary()));
FTSRestResponse.configureTableColumn(getResultTable(),
wantedFields, tempUserPrefs);
getResultTable().setVisible(true);
totalResultSetCount = resultList.getNumberOfItemsFound();
resultSetCount = resultList.getSearchSummary() == null ? 0
: resultList.getSearchSummary().size();
- String result = (resultSetCount > 0) ? MessageManager
- .getString("label.results") : MessageManager
- .getString("label.result");
+ String result = (resultSetCount > 0)
+ ? MessageManager.getString("label.results")
+ : MessageManager.getString("label.result");
if (isPaginationEnabled() && resultSetCount > 0)
{
- updateSearchFrameTitle(defaultFTSFrameTitle
- + " - "
- + result
+ updateSearchFrameTitle(defaultFTSFrameTitle + " - " + result
+ " "
+ totalNumberformatter.format((Number) (offSet + 1))
+ " to "
.format((Number) (offSet + resultSetCount))
+ " of "
+ totalNumberformatter
- .format((Number) totalResultSetCount) + " "
- + " (" + (endTime - startTime) + " milli secs)");
+ .format((Number) totalResultSetCount)
+ + " " + " (" + (endTime - startTime) + " milli secs)");
}
else
{
foundSearchTerms = foundSearchTermsBuilder.toString();
if (foundSearchTerms.contains(" OR "))
{
- foundSearchTerms = foundSearchTerms.substring(
- targetField.length() + 1, endIndex);
+ foundSearchTerms = foundSearchTerms
+ .substring(targetField.length() + 1, endIndex);
}
}
else if (enteredText.contains(":"))
int primaryKeyColIndex = 0;
try
{
- primaryKeyColIndex = getFTSRestClient().getPrimaryKeyColumIndex(
- wantedFields, false);
+ primaryKeyColIndex = getFTSRestClient()
+ .getPrimaryKeyColumIndex(wantedFields, false);
} catch (Exception e)
{
e.printStackTrace();
String searchTerm = getTypedText();
for (int summaryRow : selectedRows)
{
- String idStr = getResultTable().getValueAt(summaryRow,
- primaryKeyColIndex).toString();
+ String idStr = getResultTable()
+ .getValueAt(summaryRow, primaryKeyColIndex).toString();
selectedIdsSet.add(getPDBIdwithSpecifiedChain(idStr, searchTerm));
}
return tempUserPrefs;
}
-
@Override
public String getCacheKey()
{
return PDB_FTS_CACHE_KEY;
}
-
}
ClientConfig clientConfig = new DefaultClientConfig();
Client client = Client.create(clientConfig);
- String wantedFields = getDataColumnsFieldsAsCommaDelimitedString(pdbRestRequest
- .getWantedFields());
- int responseSize = (pdbRestRequest.getResponseSize() == 0) ? getDefaultResponsePageSize()
+ String wantedFields = getDataColumnsFieldsAsCommaDelimitedString(
+ pdbRestRequest.getWantedFields());
+ int responseSize = (pdbRestRequest.getResponseSize() == 0)
+ ? getDefaultResponsePageSize()
: pdbRestRequest.getResponseSize();
int offSet = pdbRestRequest.getOffSet();
String sortParam = null;
}
}
- String facetPivot = (pdbRestRequest.getFacetPivot() == null || pdbRestRequest
- .getFacetPivot().isEmpty()) ? "" : pdbRestRequest
- .getFacetPivot();
- String facetPivotMinCount = String.valueOf(pdbRestRequest
- .getFacetPivotMinCount());
+ String facetPivot = (pdbRestRequest.getFacetPivot() == null
+ || pdbRestRequest.getFacetPivot().isEmpty()) ? ""
+ : pdbRestRequest.getFacetPivot();
+ String facetPivotMinCount = String
+ .valueOf(pdbRestRequest.getFacetPivotMinCount());
String query = pdbRestRequest.getFieldToSearchBy()
+ pdbRestRequest.getSearchTerm()
.queryParam("q", query).queryParam("sort", sortParam);
}
// Execute the REST request
- ClientResponse clientResponse = webResource.accept(
- MediaType.APPLICATION_JSON).get(ClientResponse.class);
+ ClientResponse clientResponse = webResource
+ .accept(MediaType.APPLICATION_JSON).get(ClientResponse.class);
// Get the JSON string from the response object
String responseString = clientResponse.getEntity(String.class);
if (exceptionMsg.contains("SocketException"))
{
// No internet connection
- throw new Exception(
- MessageManager
- .getString("exception.unable_to_detect_internet_connection"));
+ throw new Exception(MessageManager.getString(
+ "exception.unable_to_detect_internet_connection"));
}
else if (exceptionMsg.contains("UnknownHostException"))
{
.parse(pdbJsonResponseString);
JSONObject pdbResponse = (JSONObject) jsonObj.get("response");
- String queryTime = ((JSONObject) jsonObj.get("responseHeader")).get(
- "QTime").toString();
+ String queryTime = ((JSONObject) jsonObj.get("responseHeader"))
+ .get("QTime").toString();
int numFound = Integer
.valueOf(pdbResponse.get("numFound").toString());
if (numFound > 0)
Collection<FTSDataColumnI> diplayFields = request.getWantedFields();
SequenceI associatedSeq = request.getAssociatedSequence();
int colCounter = 0;
- summaryRowData = new Object[(associatedSeq != null) ? diplayFields
- .size() + 1 : diplayFields.size()];
+ summaryRowData = new Object[(associatedSeq != null)
+ ? diplayFields.size() + 1
+ : diplayFields.size()];
if (associatedSeq != null)
{
associatedSequence = associatedSeq;
try
{
summaryRowData[colCounter++] = (field.getDataType()
- .getDataTypeClass() == Integer.class) ? Integer
- .valueOf(fieldData) : (field.getDataType()
- .getDataTypeClass() == Double.class) ? Double
- .valueOf(fieldData) : sanitiseData(fieldData);
+ .getDataTypeClass() == Integer.class)
+ ? Integer.valueOf(fieldData)
+ : (field.getDataType()
+ .getDataTypeClass() == Double.class)
+ ? Double.valueOf(fieldData)
+ : sanitiseData(fieldData);
} catch (Exception e)
{
e.printStackTrace();
|| allDefaultDisplayedStructureDataColumns.isEmpty())
{
allDefaultDisplayedStructureDataColumns = new ArrayList<FTSDataColumnI>();
- allDefaultDisplayedStructureDataColumns.addAll(super
- .getAllDefaultDisplayedFTSDataColumns());
+ allDefaultDisplayedStructureDataColumns
+ .addAll(super.getAllDefaultDisplayedFTSDataColumns());
}
return allDefaultDisplayedStructureDataColumns;
}
ClientConfig clientConfig = new DefaultClientConfig();
Client client = Client.create(clientConfig);
- String wantedFields = getDataColumnsFieldsAsCommaDelimitedString(uniportRestRequest
- .getWantedFields());
- int responseSize = (uniportRestRequest.getResponseSize() == 0) ? getDefaultResponsePageSize()
+ String wantedFields = getDataColumnsFieldsAsCommaDelimitedString(
+ uniportRestRequest.getWantedFields());
+ int responseSize = (uniportRestRequest.getResponseSize() == 0)
+ ? getDefaultResponsePageSize()
: uniportRestRequest.getResponseSize();
int offSet = uniportRestRequest.getOffSet();
}
else
{
- query = uniportRestRequest.getFieldToSearchBy().equalsIgnoreCase(
- "Search All") ? uniportRestRequest.getSearchTerm()
- + " or mnemonic:" + uniportRestRequest.getSearchTerm()
- : uniportRestRequest.getFieldToSearchBy() + ":"
- + uniportRestRequest.getSearchTerm();
+ query = uniportRestRequest.getFieldToSearchBy()
+ .equalsIgnoreCase("Search All")
+ ? uniportRestRequest.getSearchTerm()
+ + " or mnemonic:"
+ + uniportRestRequest.getSearchTerm()
+ : uniportRestRequest.getFieldToSearchBy() + ":"
+ + uniportRestRequest.getSearchTerm();
}
WebResource webResource = null;
.queryParam("offset", String.valueOf(offSet))
.queryParam("sort", "score").queryParam("query", query);
// Execute the REST request
- ClientResponse clientResponse = webResource.accept(
- MediaType.TEXT_PLAIN).get(ClientResponse.class);
+ ClientResponse clientResponse = webResource
+ .accept(MediaType.TEXT_PLAIN).get(ClientResponse.class);
String uniProtTabDelimittedResponseString = clientResponse
.getEntity(String.class);
// Make redundant objects eligible for garbage collection to conserve
throw new Exception(errorMessage);
}
- int xTotalResults = Integer.valueOf(clientResponse.getHeaders()
- .get("X-Total-Results").get(0));
+ int xTotalResults = Integer.valueOf(
+ clientResponse.getHeaders().get("X-Total-Results").get(0));
clientResponse = null;
client = null;
return parseUniprotResponse(uniProtTabDelimittedResponseString,
if (exceptionMsg.contains("SocketException"))
{
// No internet connection
- throw new Exception(
- MessageManager
- .getString("exception.unable_to_detect_internet_connection"));
+ throw new Exception(MessageManager.getString(
+ "exception.unable_to_detect_internet_connection"));
}
else if (exceptionMsg.contains("UnknownHostException"))
{
try
{
summaryRowData[colCounter++] = (field.getDataType()
- .getDataTypeClass() == Integer.class) ? Integer
- .valueOf(fieldData.replace(",", ""))
- : (field.getDataType().getDataTypeClass() == Double.class) ? Double
- .valueOf(fieldData) : fieldData;
+ .getDataTypeClass() == Integer.class)
+ ? Integer.valueOf(fieldData.replace(",", ""))
+ : (field.getDataType()
+ .getDataTypeClass() == Double.class)
+ ? Double.valueOf(fieldData)
+ : fieldData;
} catch (Exception e)
{
e.printStackTrace();
private static String defaultFTSFrameTitle = MessageManager
.getString("label.uniprot_sequence_fetcher");
-
private static Map<String, Integer> tempUserPrefs = new HashMap<String, Integer>();
private static final String UNIPROT_FTS_CACHE_KEY = "CACHE.UNIPROT_FTS";
pageLimit = UniProtFTSRestClient.getInstance()
.getDefaultResponsePageSize();
this.seqFetcher = seqFetcher;
- this.progressIndicator = (seqFetcher == null) ? null : seqFetcher
- .getProgressIndicator();
+ this.progressIndicator = (seqFetcher == null) ? null
+ : seqFetcher.getProgressIndicator();
}
@Override
if (resultList.getSearchSummary() != null
&& resultList.getSearchSummary().size() > 0)
{
- getResultTable().setModel(
- FTSRestResponse.getTableModel(request,
- resultList.getSearchSummary()));
+ getResultTable().setModel(FTSRestResponse.getTableModel(request,
+ resultList.getSearchSummary()));
FTSRestResponse.configureTableColumn(getResultTable(),
wantedFields, tempUserPrefs);
getResultTable().setVisible(true);
totalResultSetCount = resultList.getNumberOfItemsFound();
resultSetCount = resultList.getSearchSummary() == null ? 0
: resultList.getSearchSummary().size();
- String result = (resultSetCount > 0) ? MessageManager
- .getString("label.results") : MessageManager
- .getString("label.result");
+ String result = (resultSetCount > 0)
+ ? MessageManager.getString("label.results")
+ : MessageManager.getString("label.result");
if (isPaginationEnabled() && resultSetCount > 0)
{
- updateSearchFrameTitle(defaultFTSFrameTitle
- + " - "
- + result
+ updateSearchFrameTitle(defaultFTSFrameTitle + " - " + result
+ " "
+ totalNumberformatter.format((Number) (offSet + 1))
+ " to "
.format((Number) (offSet + resultSetCount))
+ " of "
+ totalNumberformatter
- .format((Number) totalResultSetCount) + " "
- + " (" + (endTime - startTime) + " milli secs)");
+ .format((Number) totalResultSetCount)
+ + " " + " (" + (endTime - startTime) + " milli secs)");
}
else
{
int primaryKeyColIndex = 0;
try
{
- primaryKeyColIndex = getFTSRestClient().getPrimaryKeyColumIndex(
- wantedFields, false);
+ primaryKeyColIndex = getFTSRestClient()
+ .getPrimaryKeyColumIndex(wantedFields, false);
} catch (Exception e)
{
e.printStackTrace();
int[] selectedRows = getResultTable().getSelectedRows();
for (int summaryRow : selectedRows)
{
- String idStr = getResultTable().getValueAt(summaryRow,
- primaryKeyColIndex).toString();
+ String idStr = getResultTable()
+ .getValueAt(summaryRow, primaryKeyColIndex).toString();
selectedIdsSet.add(idStr);
}
selectedIdsSet.addAll(paginatorCart);
import javax.swing.JOptionPane;
@SuppressWarnings("serial")
-public class AlignExportSettings extends GAlignExportSettings implements
- AlignExportSettingI
+public class AlignExportSettings extends GAlignExportSettings
+ implements AlignExportSettingI
{
boolean cancelled = false;
{
JOptionPane pane = new JOptionPane(null, JOptionPane.DEFAULT_OPTION,
- JvOptionPane.DEFAULT_OPTION, null, new Object[] { this });
+ JvOptionPane.DEFAULT_OPTION, null, new Object[]
+ { this });
dialog = pane.createDialog(Desktop.desktop,
MessageManager.getString("label.export_settings"));
dialog.addWindowListener(new WindowAdapter()
* @param height
* height of frame.
*/
- public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
- int width, int height)
+ public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
+ int height)
{
this(al, hiddenColumns, width, height, null);
}
* @param sequenceSetId
* (may be null)
*/
- public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
- int width, int height, String sequenceSetId)
+ public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
+ int height, String sequenceSetId)
{
this(al, hiddenColumns, width, height, sequenceSetId, null);
}
* @param viewId
* (may be null)
*/
- public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
- int width, int height, String sequenceSetId, String viewId)
+ public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
+ int height, String sequenceSetId, String viewId)
{
setSize(width, height);
public void keyPressed(KeyEvent evt)
{
if (viewport.cursorMode
- && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
- .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
- .getKeyCode() <= KeyEvent.VK_NUMPAD9))
+ && ((evt.getKeyCode() >= KeyEvent.VK_0
+ && evt.getKeyCode() <= KeyEvent.VK_9)
+ || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
+ && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
&& Character.isDigit(evt.getKeyChar()))
{
alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
case KeyEvent.VK_LEFT:
if (evt.isAltDown() || !viewport.cursorMode)
{
- slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
+ slideSequences(false,
+ alignPanel.getSeqPanel().getKeyboardNo1());
}
else
{
case KeyEvent.VK_SPACE:
if (viewport.cursorMode)
{
- alignPanel.getSeqPanel().insertGapAtCursor(
- evt.isControlDown() || evt.isShiftDown()
- || evt.isAltDown());
+ alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
+ || evt.isShiftDown() || evt.isAltDown());
}
break;
}
else
{
- alignPanel.getSeqPanel().deleteGapAtCursor(
- evt.isControlDown() || evt.isShiftDown()
- || evt.isAltDown());
+ alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
+ || evt.isShiftDown() || evt.isAltDown());
}
break;
case KeyEvent.VK_F2:
viewport.cursorMode = !viewport.cursorMode;
- statusBar.setText(MessageManager.formatMessage(
- "label.keyboard_editing_mode",
- new String[] { (viewport.cursorMode ? "on" : "off") }));
+ statusBar.setText(MessageManager
+ .formatMessage("label.keyboard_editing_mode", new String[]
+ { (viewport.cursorMode ? "on" : "off") }));
if (viewport.cursorMode)
{
alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
case KeyEvent.VK_LEFT:
if (evt.isAltDown() || !viewport.cursorMode)
{
- viewport.firePropertyChange("alignment", null, viewport
- .getAlignment().getSequences());
+ viewport.firePropertyChange("alignment", null,
+ viewport.getAlignment().getSequences());
}
break;
case KeyEvent.VK_RIGHT:
if (evt.isAltDown() || !viewport.cursorMode)
{
- viewport.firePropertyChange("alignment", null, viewport
- .getAlignment().getSequences());
+ viewport.firePropertyChange("alignment", null,
+ viewport.getAlignment().getSequences());
}
break;
}
@Override
public void run()
{
- System.err
- .println("Rebuild WS Menu for service change");
+ System.err.println(
+ "Rebuild WS Menu for service change");
BuildWebServiceMenu();
}
showReverse.setVisible(nucleotide);
showReverseComplement.setVisible(nucleotide);
conservationMenuItem.setEnabled(!nucleotide);
- modifyConservation.setEnabled(!nucleotide
- && conservationMenuItem.isSelected());
+ modifyConservation
+ .setEnabled(!nucleotide && conservationMenuItem.isSelected());
showGroupConservation.setEnabled(!nucleotide);
- showComplementMenuItem.setText(nucleotide ? MessageManager
- .getString("label.protein") : MessageManager
- .getString("label.nucleotide"));
+ showComplementMenuItem
+ .setText(nucleotide ? MessageManager.getString("label.protein")
+ : MessageManager.getString("label.nucleotide"));
}
/**
Desktop.instance.closeAssociatedWindows();
FileLoader loader = new FileLoader();
- DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
+ DataSourceType protocol = fileName.startsWith("http:")
+ ? DataSourceType.URL
: DataSourceType.FILE;
loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
}
Rectangle bounds = this.getBounds();
FileLoader loader = new FileLoader();
- DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
+ DataSourceType protocol = fileName.startsWith("http:")
+ ? DataSourceType.URL
: DataSourceType.FILE;
AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
protocol, currentFileFormat);
@Override
public void addFromText_actionPerformed(ActionEvent e)
{
- Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
- .getAlignPanel());
+ Desktop.instance
+ .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
}
@Override
@Override
public void saveAs_actionPerformed(ActionEvent e)
{
- String format = currentFileFormat == null ? null : currentFileFormat
- .getName();
- JalviewFileChooser chooser = JalviewFileChooser.forWrite(
- Cache.getProperty("LAST_DIRECTORY"), format);
+ String format = currentFileFormat == null ? null
+ : currentFileFormat.getName();
+ JalviewFileChooser chooser = JalviewFileChooser
+ .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager
- .getString("label.save_alignment_to_file"));
+ chooser.setDialogTitle(
+ MessageManager.getString("label.save_alignment_to_file"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
currentFileFormat = chooser.getSelectedFormat();
while (currentFileFormat == null)
{
- JvOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- MessageManager
- .getString("label.select_file_format_before_saving"),
- MessageManager
- .getString("label.file_format_not_specified"),
- JvOptionPane.WARNING_MESSAGE);
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString(
+ "label.select_file_format_before_saving"),
+ MessageManager.getString("label.file_format_not_specified"),
+ JvOptionPane.WARNING_MESSAGE);
currentFileFormat = chooser.getSelectedFormat();
value = chooser.showSaveDialog(this);
if (value != JalviewFileChooser.APPROVE_OPTION)
if (shortName.indexOf(java.io.File.separatorChar) > -1)
{
- shortName = shortName.substring(shortName
- .lastIndexOf(java.io.File.separatorChar) + 1);
+ shortName = shortName.substring(
+ shortName.lastIndexOf(java.io.File.separatorChar) + 1);
}
success = new Jalview2XML().saveAlignment(this, file, shortName);
statusBar.setText(MessageManager.formatMessage(
- "label.successfully_saved_to_file_in_format", new Object[] {
- fileName, format }));
+ "label.successfully_saved_to_file_in_format", new Object[]
+ { fileName, format }));
}
else
}
FormatAdapter f = new FormatAdapter(alignPanel,
exportData.getSettings());
- String output = f.formatSequences(
- format,
- exportData.getAlignment(), // class cast exceptions will
+ String output = f.formatSequences(format, exportData.getAlignment(), // class
+ // cast
+ // exceptions
+ // will
// occur in the distant future
exportData.getOmitHidden(), exportData.getStartEndPostions(),
- f.getCacheSuffixDefault(format), viewport.getAlignment()
- .getHiddenColumns());
+ f.getCacheSuffixDefault(format),
+ viewport.getAlignment().getHiddenColumns());
if (output == null)
{
out.close();
this.setTitle(file);
statusBar.setText(MessageManager.formatMessage(
- "label.successfully_saved_to_file_in_format",
- new Object[] { fileName, format.getName() }));
+ "label.successfully_saved_to_file_in_format", new Object[]
+ { fileName, format.getName() }));
} catch (Exception ex)
{
success = false;
if (!success)
{
JvOptionPane.showInternalMessageDialog(this, MessageManager
- .formatMessage("label.couldnt_save_file",
- new Object[] { fileName }), MessageManager
- .getString("label.error_saving_file"),
+ .formatMessage("label.couldnt_save_file", new Object[]
+ { fileName }),
+ MessageManager.getString("label.error_saving_file"),
JvOptionPane.WARNING_MESSAGE);
}
@Override
protected void outputText_actionPerformed(ActionEvent e)
{
- FileFormatI fileFormat = FileFormats.getInstance().forName(
- e.getActionCommand());
+ FileFormatI fileFormat = FileFormats.getInstance()
+ .forName(e.getActionCommand());
AlignmentExportData exportData = getAlignmentForExport(fileFormat,
viewport, null);
if (exportData.getSettings().isCancelled())
cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
.formatSequences(format, exportData.getAlignment(),
exportData.getOmitHidden(),
- exportData
- .getStartEndPostions(), viewport
- .getAlignment().getHiddenColumns()));
- Desktop.addInternalFrame(cap, MessageManager.formatMessage(
- "label.alignment_output_command",
- new Object[] { e.getActionCommand() }), 600, 500);
+ exportData.getStartEndPostions(),
+ viewport.getAlignment().getHiddenColumns()));
+ Desktop.addInternalFrame(cap, MessageManager
+ .formatMessage("label.alignment_output_command", new Object[]
+ { e.getActionCommand() }), 600, 500);
} catch (OutOfMemoryError oom)
{
- new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
+ new OOMWarning("Outputting alignment as " + e.getActionCommand(),
+ oom);
cap.dispose();
}
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager
- .getString("label.load_jalview_annotations"));
- chooser.setToolTipText(MessageManager
- .getString("label.load_jalview_annotations"));
+ chooser.setDialogTitle(
+ MessageManager.getString("label.load_jalview_annotations"));
+ chooser.setToolTipText(
+ MessageManager.getString("label.load_jalview_annotations"));
int value = chooser.showOpenDialog(null);
{
undoMenuItem.setEnabled(true);
CommandI command = viewport.getHistoryList().peek();
- undoMenuItem.setText(MessageManager.formatMessage(
- "label.undo_command",
- new Object[] { command.getDescription() }));
+ undoMenuItem.setText(MessageManager
+ .formatMessage("label.undo_command", new Object[]
+ { command.getDescription() }));
}
else
{
redoMenuItem.setEnabled(true);
CommandI command = viewport.getRedoList().peek();
- redoMenuItem.setText(MessageManager.formatMessage(
- "label.redo_command",
- new Object[] { command.getDescription() }));
+ redoMenuItem.setText(MessageManager
+ .formatMessage("label.redo_command", new Object[]
+ { command.getDescription() }));
}
else
{
{
if (originalSource != viewport)
{
- Cache.log
- .warn("Implementation worry: mismatch of viewport origin for undo");
+ Cache.log.warn(
+ "Implementation worry: mismatch of viewport origin for undo");
}
originalSource.updateHiddenColumns();
// originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
// && viewport.getColumnSelection().getHiddenColumns() != null &&
// viewport.getColumnSelection()
// .getHiddenColumns().size() > 0);
- originalSource.firePropertyChange("alignment", null, originalSource
- .getAlignment().getSequences());
+ originalSource.firePropertyChange("alignment", null,
+ originalSource.getAlignment().getSequences());
}
}
if (originalSource != viewport)
{
- Cache.log
- .warn("Implementation worry: mismatch of viewport origin for redo");
+ Cache.log.warn(
+ "Implementation worry: mismatch of viewport origin for redo");
}
originalSource.updateHiddenColumns();
// originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
// && viewport.getColumnSelection().getHiddenColumns() != null &&
// viewport.getColumnSelection()
// .getHiddenColumns().size() > 0);
- originalSource.firePropertyChange("alignment", null, originalSource
- .getAlignment().getSequences());
+ originalSource.firePropertyChange("alignment", null,
+ originalSource.getAlignment().getSequences());
}
}
{
EditCommand editCommand = (EditCommand) command;
al = editCommand.getAlignment();
- List<Component> comps = PaintRefresher.components.get(viewport
- .getSequenceSetId());
+ List<Component> comps = PaintRefresher.components
+ .get(viewport.getSequenceSetId());
for (Component comp : comps)
{
List<SequenceI> sg = new ArrayList<>();
if (viewport.cursorMode)
{
- sg.add(viewport.getAlignment().getSequenceAt(
- alignPanel.getSeqPanel().seqCanvas.cursorY));
+ sg.add(viewport.getAlignment()
+ .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
}
else if (viewport.getSelectionGroup() != null
&& viewport.getSelectionGroup().getSize() != viewport
.getAlignment().getHeight())
{
- sg = viewport.getSelectionGroup().getSequences(
- viewport.getHiddenRepSequences());
+ sg = viewport.getSelectionGroup()
+ .getSequences(viewport.getHiddenRepSequences());
}
if (sg.size() < 1)
SlideSequencesCommand ssc;
if (right)
{
- ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
- size, viewport.getGapCharacter());
+ ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
+ viewport.getGapCharacter());
}
else
{
- ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
- size, viewport.getGapCharacter());
+ ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
+ viewport.getGapCharacter());
}
int groupAdjustment = 0;
if (!inSplitFrame && historyList != null && historyList.size() > 0
&& historyList.peek() instanceof SlideSequencesCommand)
{
- appendHistoryItem = ssc
- .appendSlideCommand((SlideSequencesCommand) historyList
- .peek());
+ appendHistoryItem = ssc.appendSlideCommand(
+ (SlideSequencesCommand) historyList.peek());
}
if (!appendHistoryItem)
Toolkit.getDefaultToolkit().getSystemClipboard()
.setContents(new StringSelection(""), null);
- Toolkit.getDefaultToolkit().getSystemClipboard()
- .setContents(ss, Desktop.instance);
+ Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
+ Desktop.instance);
} catch (OutOfMemoryError er)
{
new OOMWarning("copying region", er);
{
if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
{
- hiddenColumns.add(new int[] { region[0] - hiddenOffset,
- region[1] - hiddenOffset });
+ hiddenColumns
+ .add(new int[]
+ { region[0] - hiddenOffset, region[1] - hiddenOffset });
}
}
}
Desktop.jalviewClipboard = new Object[] { seqs,
viewport.getAlignment().getDataset(), hiddenColumns };
statusBar.setText(MessageManager.formatMessage(
- "label.copied_sequences_to_clipboard", new Object[] { Integer
- .valueOf(seqs.length).toString() }));
+ "label.copied_sequences_to_clipboard", new Object[]
+ { Integer.valueOf(seqs.length).toString() }));
}
/**
{
// copy and derive new dataset sequence
sequences[i] = sequences[i].deriveSequence();
- alignment.getDataset().addSequence(
- sequences[i].getDatasetSequence());
+ alignment.getDataset()
+ .addSequence(sequences[i].getDatasetSequence());
// TODO: avoid creation of duplicate dataset sequences with a
// 'contains' method using SequenceI.equals()/SequenceI.contains()
}
annotationAdded = true;
if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
{
- AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
+ AlignmentAnnotation newann = new AlignmentAnnotation(
+ alann[i]);
if (newann.graphGroup > -1)
{
if (newGraphGroups.size() <= newann.graphGroup
|| newGraphGroups.get(newann.graphGroup) == null)
{
- for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
+ for (int q = newGraphGroups
+ .size(); q <= newann.graphGroup; q++)
{
newGraphGroups.add(q, null);
}
- newGraphGroups.set(newann.graphGroup, new Integer(
- ++fgroup));
+ newGraphGroups.set(newann.graphGroup,
+ new Integer(++fgroup));
}
newann.graphGroup = newGraphGroups.get(newann.graphGroup)
.intValue();
//
addHistoryItem(new EditCommand(
MessageManager.getString("label.add_sequences"),
- Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
+ Action.PASTE, sequences, 0, alignment.getWidth(),
+ alignment));
}
// Add any annotations attached to sequences
for (int i = 0; i < sequences.length; i++)
if (newGraphGroups.size() <= newann.graphGroup
|| newGraphGroups.get(newann.graphGroup) == null)
{
- for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
+ for (int q = newGraphGroups
+ .size(); q <= newann.graphGroup; q++)
{
newGraphGroups.add(q, null);
}
- newGraphGroups.set(newann.graphGroup, new Integer(
- ++fgroup));
+ newGraphGroups.set(newann.graphGroup,
+ new Integer(++fgroup));
}
newann.graphGroup = newGraphGroups.get(newann.graphGroup)
.intValue();
// was
// duplicated
// earlier
- alignment
- .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
+ alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
+ a);
}
}
}
// >>>This is a fix for the moment, until a better solution is
// found!!<<<
af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
- .transferSettings(
- alignPanel.getSeqPanel().seqCanvas
- .getFeatureRenderer());
+ .transferSettings(alignPanel.getSeqPanel().seqCanvas
+ .getFeatureRenderer());
// TODO: maintain provenance of an alignment, rather than just make the
// title a concatenation of operations.
{
try
{
- AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
- .getAlignment(), -1);
+ AlignmentI alignment = AlignmentUtils
+ .expandContext(getViewport().getAlignment(), -1);
AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
DEFAULT_HEIGHT);
String newtitle = new String("Flanking alignment");
// >>>This is a fix for the moment, until a better solution is
// found!!<<<
af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
- .transferSettings(
- alignPanel.getSeqPanel().seqCanvas
- .getFeatureRenderer());
+ .transferSettings(alignPanel.getSeqPanel().seqCanvas
+ .getFeatureRenderer());
// TODO: maintain provenance of an alignment, rather than just make the
// title a concatenation of operations.
*/
if (sg.getSize() == viewport.getAlignment().getHeight())
{
- boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
- .getAlignment().getWidth()) ? true : false;
+ boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
+ + 1) == viewport.getAlignment().getWidth()) ? true : false;
if (isEntireAlignWidth)
{
int confirm = JvOptionPane.showConfirmDialog(this,
viewport.sendSelection();
viewport.getAlignment().deleteGroup(sg);
- viewport.firePropertyChange("alignment", null, viewport.getAlignment()
- .getSequences());
+ viewport.firePropertyChange("alignment", null,
+ viewport.getAlignment().getSequences());
if (viewport.getAlignment().getHeight() < 1)
{
try
SequenceI[] seqs;
if (viewport.getSelectionGroup() != null)
{
- seqs = viewport.getSelectionGroup().getSequencesAsArray(
- viewport.getHiddenRepSequences());
+ seqs = viewport.getSelectionGroup()
+ .getSequencesAsArray(viewport.getHiddenRepSequences());
}
else
{
column, viewport.getAlignment());
}
- statusBar.setText(MessageManager.formatMessage(
- "label.removed_columns",
- new String[] { Integer.valueOf(trimRegion.getSize())
- .toString() }));
+ statusBar.setText(MessageManager
+ .formatMessage("label.removed_columns", new String[]
+ { Integer.valueOf(trimRegion.getSize()).toString() }));
addHistoryItem(trimRegion);
}
}
- viewport.firePropertyChange("alignment", null, viewport
- .getAlignment().getSequences());
+ viewport.firePropertyChange("alignment", null,
+ viewport.getAlignment().getSequences());
}
}
SequenceI[] seqs;
if (viewport.getSelectionGroup() != null)
{
- seqs = viewport.getSelectionGroup().getSequencesAsArray(
- viewport.getHiddenRepSequences());
+ seqs = viewport.getSelectionGroup()
+ .getSequencesAsArray(viewport.getHiddenRepSequences());
start = viewport.getSelectionGroup().getStartRes();
end = viewport.getSelectionGroup().getEndRes();
}
addHistoryItem(removeGapCols);
- statusBar.setText(MessageManager.formatMessage(
- "label.removed_empty_columns",
- new Object[] { Integer.valueOf(removeGapCols.getSize())
- .toString() }));
+ statusBar.setText(MessageManager
+ .formatMessage("label.removed_empty_columns", new Object[]
+ { Integer.valueOf(removeGapCols.getSize()).toString() }));
// This is to maintain viewport position on first residue
// of first sequence
// if (viewport.hasHiddenColumns)
// viewport.getColumnSelection().compensateForEdits(shifts);
vpRanges.setStartRes(seq.findIndex(startRes) - 1);
- viewport.firePropertyChange("alignment", null, viewport.getAlignment()
- .getSequences());
+ viewport.firePropertyChange("alignment", null,
+ viewport.getAlignment().getSequences());
}
SequenceI[] seqs;
if (viewport.getSelectionGroup() != null)
{
- seqs = viewport.getSelectionGroup().getSequencesAsArray(
- viewport.getHiddenRepSequences());
+ seqs = viewport.getSelectionGroup()
+ .getSequencesAsArray(viewport.getHiddenRepSequences());
start = viewport.getSelectionGroup().getStartRes();
end = viewport.getSelectionGroup().getEndRes();
}
vpRanges.setStartRes(seq.findIndex(startRes) - 1);
- viewport.firePropertyChange("alignment", null, viewport.getAlignment()
- .getSequences());
+ viewport.firePropertyChange("alignment", null,
+ viewport.getAlignment().getSequences());
}
public void padGapsMenuitem_actionPerformed(ActionEvent e)
{
viewport.setPadGaps(padGapsMenuitem.isSelected());
- viewport.firePropertyChange("alignment", null, viewport.getAlignment()
- .getSequences());
+ viewport.firePropertyChange("alignment", null,
+ viewport.getAlignment().getSequences());
}
/**
}
String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
- List<Component> comps = PaintRefresher.components.get(viewport
- .getSequenceSetId());
+ List<Component> comps = PaintRefresher.components
+ .get(viewport.getSequenceSetId());
List<String> existingNames = getExistingViewNames(comps);
// Hide everything by the current selection - this is a hack - we do the
// invert and then hide
// first check that there will be visible columns after the invert.
- if (viewport.hasSelectedColumns()
- || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
- .getEndRes()))
+ if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
+ && sg.getStartRes() <= sg.getEndRes()))
{
// now invert the sequence set, if required - empty selection implies
// that no hiding is required.
editPane.setEditable(false);
StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
.formatAsHtml();
- editPane.setText(MessageManager.formatMessage("label.html_content",
- new Object[] { contents.toString() }));
+ editPane.setText(
+ MessageManager.formatMessage("label.html_content", new Object[]
+ { contents.toString() }));
JInternalFrame frame = new JInternalFrame();
frame.getContentPane().add(new JScrollPane(editPane));
- Desktop.addInternalFrame(frame, MessageManager.formatMessage(
- "label.alignment_properties", new Object[] { getTitle() }),
- 500, 400);
+ Desktop.addInternalFrame(frame, MessageManager
+ .formatMessage("label.alignment_properties", new Object[]
+ { getTitle() }), 500, 400);
}
/**
JInternalFrame frame = new JInternalFrame();
final OverviewPanel overview = new OverviewPanel(alignPanel);
frame.setContentPane(overview);
- Desktop.addInternalFrame(frame, MessageManager.formatMessage(
- "label.overview_params", new Object[] { this.getTitle() }),
- true, frame.getWidth(), frame.getHeight(), true, true);
+ Desktop.addInternalFrame(frame, MessageManager
+ .formatMessage("label.overview_params", new Object[]
+ { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
+ true, true);
frame.pack();
frame.setLayer(JLayeredPane.PALETTE_LAYER);
- frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
- {
- @Override
- public void internalFrameClosed(
- javax.swing.event.InternalFrameEvent evt)
- {
- overview.dispose();
- alignPanel.setOverviewPanel(null);
- };
- });
+ frame.addInternalFrameListener(
+ new javax.swing.event.InternalFrameAdapter()
+ {
+ @Override
+ public void internalFrameClosed(
+ javax.swing.event.InternalFrameEvent evt)
+ {
+ overview.dispose();
+ alignPanel.setOverviewPanel(null);
+ };
+ });
alignPanel.setOverviewPanel(overview);
}
@Override
protected void modifyPID_actionPerformed()
{
- SliderPanel.setPIDSliderSource(alignPanel,
- viewport.getResidueShading(), alignPanel.getViewName());
+ SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
+ alignPanel.getViewName());
SliderPanel.showPIDSlider();
}
public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
- .getAlignment().getSequenceAt(0));
+ AlignmentSorter.sortByPID(viewport.getAlignment(),
+ viewport.getAlignment().getSequenceAt(0));
addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
viewport.getAlignment()));
alignPanel.paintAlignment(true);
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByID(viewport.getAlignment());
- addHistoryItem(new OrderCommand("ID Sort", oldOrder,
- viewport.getAlignment()));
+ addHistoryItem(
+ new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
if ((viewport.getSelectionGroup() == null)
|| (viewport.getSelectionGroup().getSize() < 2))
{
- JvOptionPane.showInternalMessageDialog(this, MessageManager
- .getString("label.you_must_select_least_two_sequences"),
+ JvOptionPane.showInternalMessageDialog(this,
+ MessageManager.getString(
+ "label.you_must_select_least_two_sequences"),
MessageManager.getString("label.invalid_selection"),
JvOptionPane.WARNING_MESSAGE);
}
viewport.autoCalculateConsensus = autoCalculate.isSelected();
if (viewport.autoCalculateConsensus)
{
- viewport.firePropertyChange("alignment", null, viewport
- .getAlignment().getSequences());
+ viewport.firePropertyChange("alignment", null,
+ viewport.getAlignment().getSequences());
}
}
* @param options
* parameters for the distance or similarity calculation
*/
- void newTreePanel(String type, String modelName, SimilarityParamsI options)
+ void newTreePanel(String type, String modelName,
+ SimilarityParamsI options)
{
String frameTitle = "";
TreePanel tp;
{
if (_s.getLength() < sg.getEndRes())
{
- JvOptionPane
- .showMessageDialog(
- Desktop.desktop,
- MessageManager
- .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
- MessageManager
- .getString("label.sequences_selection_not_aligned"),
- JvOptionPane.WARNING_MESSAGE);
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ MessageManager.getString(
+ "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
+ MessageManager.getString(
+ "label.sequences_selection_not_aligned"),
+ JvOptionPane.WARNING_MESSAGE);
return;
}
public void addSortByOrderMenuItem(String title,
final AlignmentOrder order)
{
- final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
- "action.by_title_param", new Object[] { title }));
+ final JMenuItem item = new JMenuItem(MessageManager
+ .formatMessage("action.by_title_param", new Object[]
+ { title }));
sort.add(item);
item.addActionListener(new java.awt.event.ActionListener()
{
// pointers
AlignmentSorter.sortBy(viewport.getAlignment(), order);
- addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
- .getAlignment()));
+ addHistoryItem(new OrderCommand(order.getName(), oldOrder,
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
return;
}
- if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
+ if (viewport.getAlignment().getAlignmentAnnotation()
+ .hashCode() != _annotationScoreVectorHash)
{
sortByAnnotScore.removeAll();
// almost certainly a quicker way to do this - but we keep it simple
{
sortByTreeMenu.removeAll();
- List<Component> comps = PaintRefresher.components.get(viewport
- .getSequenceSetId());
+ List<Component> comps = PaintRefresher.components
+ .get(viewport.getSequenceSetId());
List<TreePanel> treePanels = new ArrayList<>();
for (Component comp : comps)
{
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager
- .getString("label.select_newick_like_tree_file"));
- chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
+ chooser.setDialogTitle(
+ MessageManager.getString("label.select_newick_like_tree_file"));
+ chooser.setToolTipText(
+ MessageManager.getString("label.load_tree_file"));
int value = chooser.showOpenDialog(null);
viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
} catch (Exception ex)
{
- JvOptionPane
- .showMessageDialog(
- Desktop.desktop,
- ex.getMessage(),
- MessageManager
- .getString("label.problem_reading_tree_file"),
- JvOptionPane.WARNING_MESSAGE);
+ JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
+ MessageManager.getString("label.problem_reading_tree_file"),
+ JvOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
if (fin != null && fin.hasWarningMessage())
{
- JvOptionPane.showMessageDialog(Desktop.desktop, fin
- .getWarningMessage(), MessageManager
- .getString("label.possible_problem_with_tree_file"),
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ fin.getWarningMessage(),
+ MessageManager
+ .getString("label.possible_problem_with_tree_file"),
JvOptionPane.WARNING_MESSAGE);
}
}
}
} catch (Exception e)
{
- Cache.log
- .debug("Exception during web service menu building process.",
- e);
+ Cache.log.debug(
+ "Exception during web service menu building process.",
+ e);
}
}
});
@Override
public void actionPerformed(ActionEvent e)
{
- showProductsFor(af.viewport.getSequenceSelection(), dna, source);
+ showProductsFor(af.viewport.getSequenceSelection(), dna,
+ source);
}
});
showProducts.add(xtype);
showProducts.setEnabled(showp);
} catch (Exception e)
{
- Cache.log
- .warn("canShowProducts threw an exception - please report to help@jalview.org",
- e);
+ Cache.log.warn(
+ "canShowProducts threw an exception - please report to help@jalview.org",
+ e);
return false;
}
return showp;
* @param source
* the database to show cross-references for
*/
- protected void showProductsFor(final SequenceI[] sel,
- final boolean _odna, final String source)
+ protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
+ final String source)
{
new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
.start();
{
jalview.bin.Cache.log.error(
"Exception during translation. Please report this !", ex);
- final String msg = MessageManager
- .getString("label.error_when_translating_sequences_submit_bug_report");
+ final String msg = MessageManager.getString(
+ "label.error_when_translating_sequences_submit_bug_report");
final String errorTitle = MessageManager
.getString("label.implementation_error")
+ MessageManager.getString("label.translation_failed");
}
if (al == null || al.getHeight() == 0)
{
- final String msg = MessageManager
- .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
+ final String msg = MessageManager.getString(
+ "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
final String errorTitle = MessageManager
.getString("label.translation_failed");
JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
{
AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
af.setFileFormat(this.currentFileFormat);
- final String newTitle = MessageManager.formatMessage(
- "label.translation_of_params",
- new Object[] { this.getTitle() });
+ final String newTitle = MessageManager
+ .formatMessage("label.translation_of_params", new Object[]
+ { this.getTitle() });
af.setTitle(newTitle);
if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
{
{
// check to see if any of these files have names matching sequences in
// the alignment
- SequenceIdMatcher idm = new SequenceIdMatcher(viewport
- .getAlignment().getSequencesArray());
+ SequenceIdMatcher idm = new SequenceIdMatcher(
+ viewport.getAlignment().getSequencesArray());
/**
* Object[] { String,SequenceI}
*/
if (filesmatched.size() > 0)
{
if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
- || JvOptionPane
- .showConfirmDialog(
- this,
- MessageManager
- .formatMessage(
- "label.automatically_associate_structure_files_with_sequences_same_name",
- new Object[] { Integer
- .valueOf(
- filesmatched
- .size())
- .toString() }),
- MessageManager
- .getString("label.automatically_associate_structure_files_by_name"),
- JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
+ || JvOptionPane.showConfirmDialog(this,
+ MessageManager.formatMessage(
+ "label.automatically_associate_structure_files_with_sequences_same_name",
+ new Object[]
+ { Integer.valueOf(filesmatched.size())
+ .toString() }),
+ MessageManager.getString(
+ "label.automatically_associate_structure_files_by_name"),
+ JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
{
for (Object[] fm : filesmatched)
Desktop.instance);
if (pe != null)
{
- System.err.println("Associated file : "
- + ((String) fm[0]) + " with "
- + toassoc.getDisplayId(true));
+ System.err.println("Associated file : " + ((String) fm[0])
+ + " with " + toassoc.getDisplayId(true));
assocfiles++;
}
}
}
if (filesnotmatched.size() > 0)
{
- if (assocfiles > 0
- && (Cache.getDefault(
- "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
- .showConfirmDialog(
- this,
- "<html>"
- + MessageManager
- .formatMessage(
- "label.ignore_unmatched_dropped_files_info",
- new Object[] { Integer
- .valueOf(
- filesnotmatched
- .size())
- .toString() })
- + "</html>",
- MessageManager
- .getString("label.ignore_unmatched_dropped_files"),
- JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
+ if (assocfiles > 0 && (Cache.getDefault(
+ "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
+ || JvOptionPane.showConfirmDialog(this,
+ "<html>" + MessageManager.formatMessage(
+ "label.ignore_unmatched_dropped_files_info",
+ new Object[]
+ { Integer.valueOf(filesnotmatched.size())
+ .toString() })
+ + "</html>",
+ MessageManager.getString(
+ "label.ignore_unmatched_dropped_files"),
+ JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
{
return;
}
// if the file isn't identified, or not positively identified as some
// other filetype (PFAM is default unidentified alignment file type) then
// try to parse as annotation.
- boolean isAnnotation = (format == null || FileFormat.Pfam
- .equals(format)) ? new AnnotationFile()
- .annotateAlignmentView(viewport, file, sourceType) : false;
+ boolean isAnnotation = (format == null
+ || FileFormat.Pfam.equals(format))
+ ? new AnnotationFile().annotateAlignmentView(viewport,
+ file, sourceType)
+ : false;
if (!isAnnotation)
{
if (tcf.annotateAlignment(viewport.getAlignment(), true))
{
buildColourMenu();
- changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
+ changeColour(
+ new TCoffeeColourScheme(viewport.getAlignment()));
isAnnotation = true;
- statusBar
- .setText(MessageManager
- .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
+ statusBar.setText(MessageManager.getString(
+ "label.successfully_pasted_tcoffee_scores_to_alignment"));
}
else
{
// some problem - if no warning its probable that the ID matching
// process didn't work
- JvOptionPane
- .showMessageDialog(
- Desktop.desktop,
- tcf.getWarningMessage() == null ? MessageManager
- .getString("label.check_file_matches_sequence_ids_alignment")
- : tcf.getWarningMessage(),
- MessageManager
- .getString("label.problem_reading_tcoffee_score_file"),
- JvOptionPane.WARNING_MESSAGE);
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ tcf.getWarningMessage() == null
+ ? MessageManager.getString(
+ "label.check_file_matches_sequence_ids_alignment")
+ : tcf.getWarningMessage(),
+ MessageManager.getString(
+ "label.problem_reading_tcoffee_score_file"),
+ JvOptionPane.WARNING_MESSAGE);
}
}
else
}
} catch (Exception x)
{
- Cache.log
- .debug("Exception when processing data source as T-COFFEE score file",
- x);
+ Cache.log.debug(
+ "Exception when processing data source as T-COFFEE score file",
+ x);
tcf = null;
}
if (tcf == null)
}
if (FileFormat.ScoreMatrix == format)
{
- ScoreMatrixFile sm = new ScoreMatrixFile(new FileParse(file,
- sourceType));
+ ScoreMatrixFile sm = new ScoreMatrixFile(
+ new FileParse(file, sourceType));
sm.parse();
// todo: i18n this message
- statusBar
- .setText(MessageManager.formatMessage(
- "label.successfully_loaded_matrix",
- sm.getMatrixName()));
+ statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_loaded_matrix",
+ sm.getMatrixName()));
}
else if (FileFormat.Jnet.equals(format))
{
}
new OOMWarning(
"loading data "
- + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
- : "using " + sourceType + " from " + file)
+ + (sourceType != null
+ ? (sourceType == DataSourceType.PASTE
+ ? "from clipboard."
+ : "using " + sourceType + " from "
+ + file)
: ".")
- + (format != null ? "(parsing as '" + format
- + "' file)" : ""), oom, Desktop.desktop);
+ + (format != null
+ ? "(parsing as '" + format + "' file)"
+ : ""),
+ oom, Desktop.desktop);
}
}
final AlignViewportI peer = viewport.getCodingComplement();
if (peer != null)
{
- AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
+ AlignFrame linkedAlignFrame = ((AlignViewport) peer)
+ .getAlignPanel().alignFrame;
if (linkedAlignFrame.tabbedPane.getTabCount() > index)
{
linkedAlignFrame.tabbedPane.setSelectedIndex(index);
// here
final JMenu rfetch = new JMenu(
MessageManager.getString("action.fetch_db_references"));
- rfetch.setToolTipText(MessageManager
- .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
+ rfetch.setToolTipText(MessageManager.getString(
+ "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
webService.add(rfetch);
final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
MessageManager.getString("option.trim_retrieved_seqs"));
- trimrs.setToolTipText(MessageManager
- .getString("label.trim_retrieved_sequences"));
+ trimrs.setToolTipText(
+ MessageManager.getString("label.trim_retrieved_sequences"));
trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
trimrs.addActionListener(new ActionListener()
{
rfetch.add(trimrs);
JMenuItem fetchr = new JMenuItem(
MessageManager.getString("label.standard_databases"));
- fetchr.setToolTipText(MessageManager
- .getString("label.fetch_embl_uniprot"));
+ fetchr.setToolTipText(
+ MessageManager.getString("label.fetch_embl_uniprot"));
fetchr.addActionListener(new ActionListener()
{
{
boolean isNucleotide = alignPanel.alignFrame.getViewport()
.getAlignment().isNucleotide();
- DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
- .getSequenceSelection(), alignPanel.alignFrame, null,
+ DBRefFetcher dbRefFetcher = new DBRefFetcher(
+ alignPanel.av.getSequenceSelection(),
+ alignPanel.alignFrame, null,
alignPanel.alignFrame.featureSettings, isNucleotide);
dbRefFetcher.addListener(new FetchFinishedListenerI()
{
});
fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
MessageManager.formatMessage(
- "label.fetch_retrieve_from",
- new Object[] { src.getDbName() })));
+ "label.fetch_retrieve_from", new Object[]
+ { src.getDbName() })));
dfetch.add(fetchr);
comp++;
}
.toArray(new DbSourceProxy[0]);
// fetch all entry
DbSourceProxy src = otherdb.get(0);
- fetchr = new JMenuItem(MessageManager.formatMessage(
- "label.fetch_all_param",
- new Object[] { src.getDbSource() }));
+ fetchr = new JMenuItem(MessageManager
+ .formatMessage("label.fetch_all_param", new Object[]
+ { src.getDbSource() }));
fetchr.addActionListener(new ActionListener()
{
@Override
fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
MessageManager.formatMessage(
"label.fetch_retrieve_from_all_sources",
- new Object[] {
- Integer.valueOf(otherdb.size())
- .toString(), src.getDbSource(),
- src.getDbName() })));
+ new Object[]
+ { Integer.valueOf(otherdb.size())
+ .toString(),
+ src.getDbSource(), src.getDbName() })));
dfetch.add(fetchr);
comp++;
// and then build the rest of the individual menus
ifetch = new JMenu(MessageManager.formatMessage(
- "label.source_from_db_source",
- new Object[] { src.getDbSource() }));
+ "label.source_from_db_source", new Object[]
+ { src.getDbSource() }));
icomp = 0;
String imname = null;
int i = 0;
for (DbSourceProxy sproxy : otherdb)
{
String dbname = sproxy.getDbName();
- String sname = dbname.length() > 5 ? dbname.substring(0,
- 5) + "..." : dbname;
- String msname = dbname.length() > 10 ? dbname.substring(
- 0, 10) + "..." : dbname;
+ String sname = dbname.length() > 5
+ ? dbname.substring(0, 5) + "..."
+ : dbname;
+ String msname = dbname.length() > 10
+ ? dbname.substring(0, 10) + "..."
+ : dbname;
if (imname == null)
{
- imname = MessageManager.formatMessage(
- "label.from_msname", new Object[] { sname });
+ imname = MessageManager
+ .formatMessage("label.from_msname", new Object[]
+ { sname });
}
fetchr = new JMenuItem(msname);
final DbSourceProxy[] dassrc = { sproxy };
}
});
- fetchr.setToolTipText("<html>"
- + MessageManager.formatMessage(
+ fetchr.setToolTipText(
+ "<html>" + MessageManager.formatMessage(
"label.fetch_retrieve_from", new Object[]
{ dbname }));
ifetch.add(fetchr);
*/
public void setDisplayedView(AlignmentPanel alignmentPanel)
{
- if (!viewport.getSequenceSetId().equals(
- alignmentPanel.av.getSequenceSetId()))
+ if (!viewport.getSequenceSetId()
+ .equals(alignmentPanel.av.getSequenceSetId()))
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_cannot_show_view_alignment_frame"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_cannot_show_view_alignment_frame"));
}
- if (tabbedPane != null
- && tabbedPane.getTabCount() > 0
- && alignPanels.indexOf(alignmentPanel) != tabbedPane
- .getSelectedIndex())
+ if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
+ .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
{
tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
}
// show a warning dialog no mapped cDNA
return;
}
- AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
- .size()]));
+ AlignmentI cdna = new Alignment(
+ cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
cdna.alignAs(alignment);
String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
+ this.title;
- Desktop.addInternalFrame(alignFrame, newtitle,
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
}
/**
al = dna.reverseCdna(complement);
viewport.addAlignment(al, "");
addHistoryItem(new EditCommand(
- MessageManager.getString("label.add_sequences"),
- Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
+ MessageManager.getString("label.add_sequences"), Action.PASTE,
+ al.getSequencesArray(), 0, al.getWidth(),
viewport.getAlignment()));
} catch (Exception ex)
{
} catch (Exception ex)
{
System.err.println((ex.toString()));
- JvOptionPane
- .showInternalMessageDialog(Desktop.desktop, MessageManager
- .getString("label.couldnt_run_groovy_script"),
- MessageManager
- .getString("label.groovy_support_failed"),
- JvOptionPane.ERROR_MESSAGE);
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString("label.couldnt_run_groovy_script"),
+ MessageManager.getString("label.groovy_support_failed"),
+ JvOptionPane.ERROR_MESSAGE);
}
}
else
{
// include key modifier check in case user selects from menu
avc.markHighlightedColumns(
- (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
- true,
- (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
+ (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
+ (actionEvent.getModifiers() & (ActionEvent.META_MASK
+ | ActionEvent.CTRL_MASK)) != 0);
}
/**
colourMenu.add(textColour);
colourMenu.addSeparator();
- ColourMenuHelper.addMenuItems(colourMenu, this,
- viewport.getAlignment(), false);
+ ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
+ false);
colourMenu.addSeparator();
colourMenu.add(conservationMenuItem);
* @author $author$
* @version $Revision: 1.141 $
*/
-public class AlignViewport extends AlignmentViewport implements
- SelectionSource
+public class AlignViewport extends AlignmentViewport
+ implements SelectionSource
{
Font font;
// TODO remove these once 2.4.VAMSAS release finished
if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
{
- Cache.log.debug("Setting viewport's sequence set id : "
- + sequenceSetID);
+ Cache.log.debug(
+ "Setting viewport's sequence set id : " + sequenceSetID);
}
if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
{
// TODO remove these once 2.4.VAMSAS release finished
if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
{
- Cache.log.debug("Setting viewport's sequence set id : "
- + sequenceSetID);
+ Cache.log.debug(
+ "Setting viewport's sequence set id : " + sequenceSetID);
}
if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
{
setShowDBRefs(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
viewStyle.setSeqNameItalics(Cache.getDefault("ID_ITALICS", true));
viewStyle.setWrapAlignment(Cache.getDefault("WRAP_ALIGNMENT", false));
- viewStyle.setShowUnconserved(Cache
- .getDefault("SHOW_UNCONSERVED", false));
+ viewStyle.setShowUnconserved(
+ Cache.getDefault("SHOW_UNCONSERVED", false));
sortByTree = Cache.getDefault("SORT_BY_TREE", false);
followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true);
- sortAnnotationsBy = SequenceAnnotationOrder.valueOf(Cache.getDefault(
- Preferences.SORT_ANNOTATIONS,
- SequenceAnnotationOrder.NONE.name()));
- showAutocalculatedAbove = Cache.getDefault(
- Preferences.SHOW_AUTOCALC_ABOVE, false);
- viewStyle.setScaleProteinAsCdna(Cache.getDefault(
- Preferences.SCALE_PROTEIN_TO_CDNA, true));
+ sortAnnotationsBy = SequenceAnnotationOrder
+ .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
+ SequenceAnnotationOrder.NONE.name()));
+ showAutocalculatedAbove = Cache
+ .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
+ viewStyle.setScaleProteinAsCdna(
+ Cache.getDefault(Preferences.SCALE_PROTEIN_TO_CDNA, true));
}
void init()
showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
}
initAutoAnnotation();
- String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC
+ String colourProperty = alignment.isNucleotide()
+ ? Preferences.DEFAULT_COLOUR_NUC
: Preferences.DEFAULT_COLOUR_PROT;
String schemeName = Cache.getProperty(colourProperty);
if (schemeName == null)
schemeName = Cache.getDefault(Preferences.DEFAULT_COLOUR,
ResidueColourScheme.NONE);
}
- ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme(
- alignment, schemeName);
+ ColourSchemeI colourScheme = ColourSchemeProperty
+ .getColourScheme(alignment, schemeName);
residueShading = new ResidueShader(colourScheme);
if (colourScheme instanceof UserColourScheme)
public void sendSelection()
{
jalview.structure.StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance).sendSelection(
- new SequenceGroup(getSelectionGroup()),
+ .getStructureSelectionManager(Desktop.instance)
+ .sendSelection(new SequenceGroup(getSelectionGroup()),
new ColumnSelection(getColumnSelection()),
new HiddenColumns(getAlignment().getHiddenColumns()),
this);
*/
public AlignmentPanel getAlignPanel()
{
- AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this
- .getSequenceSetId());
+ AlignmentPanel[] aps = PaintRefresher
+ .getAssociatedPanels(this.getSequenceSetId());
for (int p = 0; aps != null && p < aps.length; p++)
{
if (aps[p].av == this)
&& pdb.getChainCode() != null)
{
if (pdbRefEntry.getChainCode().equalsIgnoreCase(
- pdb.getChainCode())
- && !choosenSeqs.contains(sq))
+ pdb.getChainCode()) && !choosenSeqs.contains(sq))
{
choosenSeqs.add(sq);
continue;
* <ul>
* <li>compute the equivalent edit on the mapped sequences</li>
* <li>apply the mapped edit</li>
- * <li>'apply' the source edit to the working copy of the source sequences</li>
+ * <li>'apply' the source edit to the working copy of the source
+ * sequences</li>
* </ul>
*
* @param command
*/
protected boolean openLinkedAlignment(AlignmentI al, String title)
{
- String[] options = new String[] {
- MessageManager.getString("action.no"),
+ String[] options = new String[] { MessageManager.getString("action.no"),
MessageManager.getString("label.split_window"),
MessageManager.getString("label.new_window"), };
final String question = JvSwingUtils.wrapTooltip(true,
AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
newAlignFrame.setTitle(title);
- newAlignFrame.statusBar.setText(MessageManager.formatMessage(
- "label.successfully_loaded_file", new Object[] { title }));
+ newAlignFrame.statusBar.setText(MessageManager
+ .formatMessage("label.successfully_loaded_file", new Object[]
+ { title }));
// TODO if we want this (e.g. to enable reload of the alignment from file),
// we will need to add parameters to the stack.
try
{
- newAlignFrame.setMaximum(jalview.bin.Cache.getDefault(
- "SHOW_FULLSCREEN", false));
+ newAlignFrame.setMaximum(
+ jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
} catch (java.beans.PropertyVetoException ex)
{
}
* is protein, the mappings to cDNA will be registered with
* StructureSelectionManager as a side-effect.
*/
- AlignFrame copyMe = new AlignFrame(complement,
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ AlignFrame copyMe = new AlignFrame(complement, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
copyMe.setTitle(getAlignPanel().alignFrame.getTitle());
AlignmentI al = newAlignFrame.viewport.getAlignment();
* @version $Revision: 1.161 $
*/
public class AlignmentPanel extends GAlignmentPanel implements
- AdjustmentListener, Printable, AlignmentViewPanel,
- ViewportListenerI
+ AdjustmentListener, Printable, AlignmentViewPanel, ViewportListenerI
{
public AlignViewport av;
// is initialised
if (av.getWrapAlignment())
{
- int widthInRes = getSeqPanel().seqCanvas
- .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
+ int widthInRes = getSeqPanel().seqCanvas.getWrappedCanvasWidth(
+ getSeqPanel().seqCanvas.getWidth());
vpRanges.setViewportWidth(widthInRes);
}
else
/ av.getCharWidth();
int heightInSeq = getSeqPanel().seqCanvas.getHeight()
/ av.getCharHeight();
-
+
vpRanges.setViewportWidth(widthInRes);
vpRanges.setViewportHeight(heightInSeq);
}
// to prevent drawing old image
FontMetrics fm = getFontMetrics(av.getFont());
- scalePanelHolder.setPreferredSize(new Dimension(10, av.getCharHeight()
- + fm.getDescent()));
- idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av
- .getCharHeight() + fm.getDescent()));
+ scalePanelHolder.setPreferredSize(
+ new Dimension(10, av.getCharHeight() + fm.getDescent()));
+ idSpaceFillerPanel1.setPreferredSize(
+ new Dimension(10, av.getCharHeight() + fm.getDescent()));
getIdPanel().getIdCanvas().gg = null;
getSeqPanel().seqCanvas.img = null;
{
Container c = new Container();
- FontMetrics fm = c.getFontMetrics(new Font(av.font.getName(),
- Font.ITALIC, av.font.getSize()));
+ FontMetrics fm = c.getFontMetrics(
+ new Font(av.font.getName(), Font.ITALIC, av.font.getSize()));
AlignmentI al = av.getAlignment();
int i = 0;
}
}
- return new Dimension(maxwidth < 0 ? idWidth : Math.min(maxwidth,
- idWidth), 12);
+ return new Dimension(
+ maxwidth < 0 ? idWidth : Math.min(maxwidth, idWidth), 12);
}
/**
/*
* Scroll down to make end of search results visible
*/
- setScrollValues(vpRanges.getStartRes(), starts + seqIndex - ends
- + 1);
+ setScrollValues(vpRanges.getStartRes(),
+ starts + seqIndex - ends + 1);
}
/*
* Else results are already visible - no need to scroll
*/
if (annotationHeight + alignmentHeight > availableHeight)
{
- annotationHeight = Math.min(annotationHeight, availableHeight - 2
- * rowHeight);
+ annotationHeight = Math.min(annotationHeight,
+ availableHeight - 2 * rowHeight);
}
}
else
}
hscroll.addNotify();
- annotationScroller.setPreferredSize(new Dimension(annotationScroller
- .getWidth(), annotationHeight));
+ annotationScroller.setPreferredSize(
+ new Dimension(annotationScroller.getWidth(), annotationHeight));
Dimension e = idPanel.getSize();
alabels.setSize(new Dimension(e.width, annotationHeight));
else
{
int widthInRes = (canvasWidth / av.getCharWidth()) - 1;
- int heightInSeq = (getSeqPanel().seqCanvas.getHeight() / av
- .getCharHeight()) - 1;
+ int heightInSeq = (getSeqPanel().seqCanvas.getHeight()
+ / av.getCharHeight()) - 1;
vpRanges.setViewportWidth(widthInRes);
vpRanges.setViewportHeight(heightInSeq);
repaint();
}
-
/**
* Adjust row/column scrollers to show a visible position in the alignment.
*
if (av.hasHiddenColumns())
{
// reset the width to exclude hidden columns
- width = av.getAlignment().getHiddenColumns().findColumnPosition(width);
+ width = av.getAlignment().getHiddenColumns()
+ .findColumnPosition(width);
}
hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
{
@Override
public void run()
- {
+ {
// When updating scrolling to use ViewportChange events, this code
// could not be validated and it is not clear if it is now being
// called. Log warning here in case it is called and unforeseen
// problems occur
- Cache.log
- .warn("Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences");
+ Cache.log.warn(
+ "Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences");
// scroll to start of panel
vpRanges.setStartRes(0);
* Get the horizontal offset to where we draw the sequences.
* This is idWidth if using a single Graphics context, else zero.
*/
- final int alignmentGraphicsOffset = idGraphics != alignmentGraphics ? 0 : idWidth;
+ final int alignmentGraphicsOffset = idGraphics != alignmentGraphics ? 0
+ : idWidth;
FontMetrics fm = getFontMetrics(av.getFont());
int charHeight = av.getCharHeight();
endSeq = alignmentHeight;
}
- int pagesHigh = ((alignmentHeight / totalSeq) + 1)
- * pageHeight;
+ int pagesHigh = ((alignmentHeight / totalSeq) + 1) * pageHeight;
if (av.isShowAnnotation())
{
{
return Printable.NO_SUCH_PAGE;
}
- final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight
- + 3;
+ final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight + 3;
/*
* draw the Scale at horizontal offset, then reset to top left (0, 0)
if (av.isRightAlignIds())
{
fm = idGraphics.getFontMetrics();
- xPos = idWidth
- - fm.stringWidth(displayId)
- - 4;
+ xPos = idWidth - fm.stringWidth(displayId) - 4;
}
idGraphics.drawString(displayId, xPos,
* draw the annotations starting at
* (idOffset, alignmentHeight) from (0, scaleHeight)
*/
- alignmentGraphics.translate(alignmentGraphicsOffset, alignmentDrawnHeight);
+ alignmentGraphics.translate(alignmentGraphicsOffset,
+ alignmentDrawnHeight);
getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av,
alignmentGraphics, -1, startRes, endRes + 1);
}
.findColumnPosition(maxwidth) - 1;
}
- int resWidth = getSeqPanel().seqCanvas.getWrappedCanvasWidth(pwidth
- - idWidth);
+ int resWidth = getSeqPanel().seqCanvas
+ .getWrappedCanvasWidth(pwidth - idWidth);
int totalHeight = cHeight * (maxwidth / resWidth + 1);
}
if (labels != null)
{
- pg.translate(-3,
- ypos + (av.getAlignment().getHeight() * av.getCharHeight()));
+ pg.translate(-3, ypos
+ + (av.getAlignment().getHeight() * av.getCharHeight()));
pg.setFont(av.getFont());
labels.drawComponent(pg, idWidth);
- pg.translate(
- +3,
- -ypos
- - (av.getAlignment().getHeight() * av
- .getCharHeight()));
+ pg.translate(+3, -ypos
+ - (av.getAlignment().getHeight() * av.getCharHeight()));
}
ypos += cHeight;
return calculateIdWidth(-1).width + 4;
}
Integer idwidth = null;
- if (onscreen
- || (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
+ if (onscreen || (idwidth = Cache
+ .getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
{
int w = getIdPanel().getWidth();
return (w > 0 ? w : calculateIdWidth().width + 4);
{
int boarderBottomOffset = 5;
long pSessionId = System.currentTimeMillis();
- headless = (System.getProperty("java.awt.headless") != null && System
- .getProperty("java.awt.headless").equals("true"));
+ headless = (System.getProperty("java.awt.headless") != null
+ && System.getProperty("java.awt.headless").equals("true"));
if (alignFrame != null && !headless)
{
if (file != null)
{
- alignFrame.setProgressBar(MessageManager.formatMessage(
- "status.saving_file", new Object[] { type.getLabel() }),
- pSessionId);
+ alignFrame.setProgressBar(MessageManager
+ .formatMessage("status.saving_file", new Object[]
+ { type.getLabel() }), pSessionId);
}
}
try
}
im = new jalview.util.ImageMaker(this, type, imageAction,
- aDimension.getWidth(), aDimension.getHeight()
- + boarderBottomOffset, file, imageTitle,
- alignFrame, pSessionId, headless);
+ aDimension.getWidth(),
+ aDimension.getHeight() + boarderBottomOffset, file,
+ imageTitle, alignFrame, pSessionId, headless);
Graphics graphics = im.getGraphics();
if (av.getWrapAlignment())
{
{
if (graphics != null)
{
- printUnwrapped(aDimension.getWidth(), aDimension.getHeight(),
- 0, graphics, graphics);
+ printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
+ graphics, graphics);
im.writeImage();
}
}
// this duplicates the calculation in getWrappedHeight but adjusts for
// offscreen idWith
width = alignFrame.getWidth() - vscroll.getPreferredSize().width
- - alignFrame.getInsets().left
- - alignFrame.getInsets().right - getVisibleIdWidth()
- + getVisibleIdWidth(false);
+ - alignFrame.getInsets().left - alignFrame.getInsets().right
+ - getVisibleIdWidth() + getVisibleIdWidth(false);
}
else
{
{
try
{
- int s, sSize = av.getAlignment().getHeight(), res, alwidth = av
- .getAlignment().getWidth(), g, gSize, f, fSize, sy;
+ int s, sSize = av.getAlignment().getHeight(), res,
+ alwidth = av.getAlignment().getWidth(), g, gSize, f, fSize,
+ sy;
PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
out.println(jalview.io.HTMLOutput.getImageMapHTML());
out.println("<img src=\"" + imageName
String triplet = null;
if (av.getAlignment().isNucleotide())
{
- triplet = ResidueProperties.nucleotideName.get(seq
- .getCharAt(res) + "");
+ triplet = ResidueProperties.nucleotideName
+ .get(seq.getCharAt(res) + "");
}
else
{
- triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(res)
- + "");
+ triplet = ResidueProperties.aa2Triplet
+ .get(seq.getCharAt(res) + "");
}
if (triplet == null)
{
text.append("<br>");
text.append(features[f].getType());
- if (features[f].getDescription() != null
- && !features[f].getType().equals(
- features[f].getDescription()))
+ if (features[f].getDescription() != null && !features[f]
+ .getType().equals(features[f].getDescription()))
{
text.append(" ").append(features[f].getDescription());
}
if (features[f].getValue("status") != null)
{
- text.append(" (").append(features[f].getValue("status"))
+ text.append(" (")
+ .append(features[f].getValue("status"))
.append(")");
}
}
@Override
/**
- * Property change event fired when a change is made to the viewport ranges
+ * Property change event fired when a change is made to the viewport ranges
* object associated with this alignment panel's viewport
*/
public void propertyChange(PropertyChangeEvent evt)
public class AnnotationChooser extends JPanel
{
- private static final Font CHECKBOX_FONT = new Font("Serif", Font.BOLD, 12);
+ private static final Font CHECKBOX_FONT = new Font("Serif", Font.BOLD,
+ 12);
private static final int MY_FRAME_WIDTH = 600;
if (oldcs instanceof AnnotationColourGradient)
{
AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
- useOriginalColours.setSelected(acg.isPredefinedColours()
- || acg.getBaseColour() != null);
+ useOriginalColours.setSelected(
+ acg.isPredefinedColours() || acg.getBaseColour() != null);
if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
{
minColour.setBackground(acg.getMinColour());
seqAssociated.setSelected(acg.isSeqAssociated());
}
- Vector<String> annotItems = getAnnotationItems(seqAssociated
- .isSelected());
+ Vector<String> annotItems = getAnnotationItems(
+ seqAssociated.isSelected());
annotations = new JComboBox<String>(annotItems);
populateThresholdComboBox(threshold);
getThreshold().setSelectedIndex(2);
break;
default:
- throw new Error(
- MessageManager
- .getString("error.implementation_error_dont_know_about_threshold_setting"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_dont_know_about_threshold_setting"));
}
thresholdIsMin.setSelected(acg.isThresholdIsMinMax());
thresholdValue.setText("" + acg.getAnnotationThreshold());
useOriginalColours.setFont(JvSwingUtils.getLabelFont());
useOriginalColours.setOpaque(false);
- useOriginalColours.setText(MessageManager
- .getString("label.use_original_colours"));
+ useOriginalColours.setText(
+ MessageManager.getString("label.use_original_colours"));
useOriginalColours.addActionListener(new ActionListener()
{
@Override
});
thresholdIsMin.setBackground(Color.white);
thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
- thresholdIsMin.setText(MessageManager
- .getString("label.threshold_minmax"));
+ thresholdIsMin
+ .setText(MessageManager.getString("label.threshold_minmax"));
thresholdIsMin.addActionListener(new ActionListener()
{
@Override
});
seqAssociated.setBackground(Color.white);
seqAssociated.setFont(JvSwingUtils.getLabelFont());
- seqAssociated.setText(MessageManager
- .getString("label.per_sequence_only"));
+ seqAssociated
+ .setText(MessageManager.getString("label.per_sequence_only"));
seqAssociated.addActionListener(new ActionListener()
{
private void setDefaultMinMax()
{
- minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
- Color.orange));
- maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
- Color.red));
+ minColour.setBackground(
+ Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
+ maxColour.setBackground(
+ Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
}
public void minColour_actionPerformed()
{
if (slider.isEnabled())
{
- if (useOriginalColours.isSelected()
- && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
+ if (useOriginalColours.isSelected() && !(av
+ .getGlobalColourScheme() instanceof AnnotationColourGradient))
{
updateView();
}
return;
}
- setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[annotations
- .getSelectedIndex()]]);
+ setCurrentAnnotation(
+ av.getAlignment().getAlignmentAnnotation()[annmap[annotations
+ .getSelectedIndex()]]);
- int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
- .getSelectedIndex());
+ int selectedThresholdItem = getSelectedThresholdItem(
+ getThreshold().getSelectedIndex());
slider.setEnabled(true);
thresholdValue.setEnabled(true);
else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
&& getCurrentAnnotation().threshold == null)
{
- getCurrentAnnotation()
- .setThreshold(
- new GraphLine(
- (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
- "Threshold", Color.black));
+ getCurrentAnnotation().setThreshold(new GraphLine(
+ (getCurrentAnnotation().graphMax
+ - getCurrentAnnotation().graphMin) / 2f,
+ "Threshold", Color.black));
}
if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
float range = getCurrentAnnotation().graphMax * ONETHOUSAND
- getCurrentAnnotation().graphMin * ONETHOUSAND;
- slider.setMinimum((int) (getCurrentAnnotation().graphMin * ONETHOUSAND));
- slider.setMaximum((int) (getCurrentAnnotation().graphMax * ONETHOUSAND));
- slider.setValue((int) (getCurrentAnnotation().threshold.value * ONETHOUSAND));
+ slider.setMinimum(
+ (int) (getCurrentAnnotation().graphMin * ONETHOUSAND));
+ slider.setMaximum(
+ (int) (getCurrentAnnotation().graphMax * ONETHOUSAND));
+ slider.setValue(
+ (int) (getCurrentAnnotation().threshold.value * ONETHOUSAND));
thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
slider.setMajorTickSpacing((int) (range / 10f));
slider.setEnabled(true);
ap.paintAlignment(true);
}
- protected boolean colorAlignmentContaining(AlignmentAnnotation currentAnn, int selectedThresholdOption)
+ protected boolean colorAlignmentContaining(AlignmentAnnotation currentAnn,
+ int selectedThresholdOption)
{
-
+
AnnotationColourGradient acg = null;
if (useOriginalColours.isSelected())
{
selectedThresholdOption);
}
acg.setSeqAssociated(seqAssociated.isSelected());
-
+
if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f)
{
acg.setPredefinedColours(true);
}
-
+
acg.setThresholdIsMinMax(thresholdIsMin.isSelected());
-
+
av.setGlobalColourScheme(acg);
-
+
if (av.getAlignment().getGroups() != null)
{
-
+
for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
if (sg.cs == null)
{
continue;
}
-
+
if (useOriginalColours.isSelected())
{
- sg.setColourScheme(new AnnotationColourGradient(currentAnn, sg
- .getColourScheme(), selectedThresholdOption));
- ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
- .isSelected());
+ sg.setColourScheme(new AnnotationColourGradient(currentAnn,
+ sg.getColourScheme(), selectedThresholdOption));
+ ((AnnotationColourGradient) sg.cs)
+ .setSeqAssociated(seqAssociated.isSelected());
}
else
{
sg.setColourScheme(new AnnotationColourGradient(currentAnn,
minColour.getBackground(), maxColour.getBackground(),
selectedThresholdOption));
- ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
- .isSelected());
+ ((AnnotationColourGradient) sg.cs)
+ .setSeqAssociated(seqAssociated.isSelected());
}
}
}
import net.miginfocom.swing.MigLayout;
@SuppressWarnings("serial")
-public class AnnotationColumnChooser extends AnnotationRowFilter implements
- ItemListener
+public class AnnotationColumnChooser extends AnnotationRowFilter
+ implements ItemListener
{
private JPanel switchableViewsPanel = new JPanel(new CardLayout());
// restore Object state from the previous session if one exists
if (lastChooser != null)
{
- currentSearchPanel = lastChooser
- .getCurrentSearchPanel();
+ currentSearchPanel = lastChooser.getCurrentSearchPanel();
currentStructureFilterPanel = lastChooser
.getCurrentStructureFilterPanel();
- annotations.setSelectedIndex(lastChooser
- .getAnnotations().getSelectedIndex());
- threshold.setSelectedIndex(lastChooser
- .getThreshold().getSelectedIndex());
- actionOption = lastChooser
- .getActionOption();
- percentThreshold.setSelected(lastChooser.percentThreshold
- .isSelected());
+ annotations.setSelectedIndex(
+ lastChooser.getAnnotations().getSelectedIndex());
+ threshold.setSelectedIndex(
+ lastChooser.getThreshold().getSelectedIndex());
+ actionOption = lastChooser.getActionOption();
+ percentThreshold
+ .setSelected(lastChooser.percentThreshold.isSelected());
}
try
super.jbInit();
JPanel thresholdPanel = new JPanel();
- thresholdPanel.setBorder(new TitledBorder(MessageManager
- .getString("label.threshold_filter")));
+ thresholdPanel.setBorder(new TitledBorder(
+ MessageManager.getString("label.threshold_filter")));
thresholdPanel.setBackground(Color.white);
thresholdPanel.setFont(JvSwingUtils.getLabelFont());
thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
if (av.getAnnotationColumnSelectionState() != null)
{
- HiddenColumns oldHidden = av
- .getAnnotationColumnSelectionState()
+ HiddenColumns oldHidden = av.getAnnotationColumnSelectionState()
.getOldHiddenColumns();
if (oldHidden != null)
{
AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
- setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
- .getSelectedIndex()]]);
+ setCurrentAnnotation(av.getAlignment()
+ .getAlignmentAnnotation()[annmap[getAnnotations()
+ .getSelectedIndex()]]);
- int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
- .getSelectedIndex());
+ int selectedThresholdItem = getSelectedThresholdItem(
+ getThreshold().getSelectedIndex());
slider.setEnabled(true);
thresholdValue.setEnabled(true);
{
if (getCurrentAnnotation().threshold == null)
{
- getCurrentAnnotation()
- .setThreshold(
- new jalview.datamodel.GraphLine(
- (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
- "Threshold", Color.black));
+ getCurrentAnnotation().setThreshold(new jalview.datamodel.GraphLine(
+ (getCurrentAnnotation().graphMax
+ - getCurrentAnnotation().graphMin) / 2f,
+ "Threshold", Color.black));
}
adjusting = true;
slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
- slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
-
+ slider.setValue(
+ (int) (getCurrentAnnotation().threshold.value * 1000));
+
setThresholdValueText();
slider.setMajorTickSpacing((int) (range / 10f));
adjusting = false;
// build filter params
- filterParams
- .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
+ filterParams.setThresholdType(
+ AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
if (getCurrentAnnotation().isQuantitative())
{
filterParams
if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
{
- filterParams
- .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
+ filterParams.setThresholdType(
+ AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
}
else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
{
- filterParams
- .setThresholdType(AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
+ filterParams.setThresholdType(
+ AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
}
}
}
{
if (!currentSearchPanel.searchBox.getUserInput().isEmpty())
{
- filterParams.setRegexString(currentSearchPanel.searchBox
- .getUserInput());
+ filterParams.setRegexString(
+ currentSearchPanel.searchBox.getUserInput());
if (currentSearchPanel.displayName.isSelected())
{
- filterParams
- .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
+ filterParams.addRegexSearchField(
+ AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
}
if (currentSearchPanel.description.isSelected())
{
- filterParams
- .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
+ filterParams.addRegexSearchField(
+ AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
}
}
}
public void selectedAnnotationChanged()
{
String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
- if (av.getAlignment()
- .getAlignmentAnnotation()[annmap[getAnnotations()
+ if (av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
.getSelectedIndex()]].isQuantitative())
{
currentView = AnnotationColumnChooser.GRAPH_VIEW;
public void syncState()
{
- if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
+ if (aColChooser
+ .getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
{
this.optionsGroup.setSelected(this.hideOption.getModel(), true);
}
}
});
- this.setBorder(new TitledBorder(MessageManager
- .getString("label.structures_filter")));
+ this.setBorder(new TitledBorder(
+ MessageManager.getString("label.structures_filter")));
JvSwingUtils.jvInitComponent(this);
this.add(all);
this.aColChooser = aColChooser;
JvSwingUtils.jvInitComponent(this);
- this.setBorder(new TitledBorder(MessageManager
- .getString("label.search_filter")));
+ this.setBorder(new TitledBorder(
+ MessageManager.getString("label.search_filter")));
searchBox.setPrototypeDisplayValue("XXXXXXXXXXXXXXXXXXXXXXX");
- searchBox.setToolTipText(MessageManager
- .getString("info.enter_search_text_here"));
+ searchBox.setToolTipText(
+ MessageManager.getString("info.enter_search_text_here"));
searchBox.getEditor().getEditorComponent()
.addKeyListener(new java.awt.event.KeyAdapter()
{
}
});
-
-
JvSwingUtils.jvInitComponent(displayName, "label.label");
displayName.addActionListener(new ActionListener()
{
String defaultTtip = MessageManager
.getString("info.enter_search_text_to_enable");
String labelTtip = MessageManager.formatMessage(
- "info.search_in_annotation_label", annotations
- .getSelectedItem().toString());
+ "info.search_in_annotation_label",
+ annotations.getSelectedItem().toString());
String descTtip = MessageManager.formatMessage(
- "info.search_in_annotation_description", annotations
- .getSelectedItem().toString());
- displayName.setToolTipText(displayName.isEnabled() ? labelTtip
- : defaultTtip);
- description.setToolTipText(description.isEnabled() ? descTtip
- : defaultTtip);
+ "info.search_in_annotation_description",
+ annotations.getSelectedItem().toString());
+ displayName.setToolTipText(
+ displayName.isEnabled() ? labelTtip : defaultTtip);
+ description.setToolTipText(
+ description.isEnabled() ? descTtip : defaultTtip);
}
}
public void exportAnnotations(AlignmentPanel ap)
{
this.ap = ap;
- annotations = ap.av.isShowAnnotation() ? null : ap.av.getAlignment()
- .getAlignmentAnnotation();
+ annotations = ap.av.isShowAnnotation() ? null
+ : ap.av.getAlignment().getAlignmentAnnotation();
wholeView = true;
startExportAnnotation();
}
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(features ? MessageManager
- .getString("label.save_features_to_file") : MessageManager
- .getString("label.save_annotation_to_file"));
+ chooser.setDialogTitle(features
+ ? MessageManager.getString("label.save_features_to_file")
+ : MessageManager.getString("label.save_annotation_to_file"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
boolean includeNonPositional = ap.av.isShowNPFeats();
if (GFFFormat.isSelected())
{
- text = new FeaturesFile().printGffFormat(ap.av.getAlignment()
- .getDataset().getSequencesArray(), displayedFeatureColours,
- true, ap.av.isShowNPFeats());
+ text = new FeaturesFile().printGffFormat(
+ ap.av.getAlignment().getDataset().getSequencesArray(),
+ displayedFeatureColours, true, ap.av.isShowNPFeats());
text = formatter.printGffFormat(sequences, featureColours, true,
includeNonPositional);
}
else
{
- text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
- .getDataset().getSequencesArray(), displayedFeatureColours,
- true, ap.av.isShowNPFeats()); // ap.av.featuresDisplayed);
- text = formatter.printJalviewFormat(sequences, featureColours,
- true, includeNonPositional);
+ text = new FeaturesFile().printJalviewFormat(
+ ap.av.getAlignment().getDataset().getSequencesArray(),
+ displayedFeatureColours, true, ap.av.isShowNPFeats()); // ap.av.featuresDisplayed);
+ text = formatter.printJalviewFormat(sequences, featureColours, true,
+ includeNonPositional);
}
}
else
{
String text = getFileContents();
cap.setText(text);
- Desktop.addInternalFrame(
- cap,
- (features ? MessageManager.formatMessage(
- "label.features_for_params",
- new String[] { ap.alignFrame.getTitle() })
- : MessageManager.formatMessage(
- "label.annotations_for_params",
- new String[] { ap.alignFrame.getTitle() })),
+ Desktop.addInternalFrame(cap, (features ? MessageManager
+ .formatMessage("label.features_for_params", new String[]
+ { ap.alignFrame.getTitle() })
+ : MessageManager.formatMessage("label.annotations_for_params",
+ new String[]
+ { ap.alignFrame.getTitle() })),
600, 500);
} catch (OutOfMemoryError oom)
{
new OOMWarning((features ? MessageManager.formatMessage(
- "label.generating_features_for_params",
- new String[] { ap.alignFrame.getTitle() })
+ "label.generating_features_for_params", new String[]
+ { ap.alignFrame.getTitle() })
: MessageManager.formatMessage(
"label.generating_annotations_for_params",
- new String[] { ap.alignFrame.getTitle() })), oom);
+ new String[]
+ { ap.alignFrame.getTitle() })),
+ oom);
cap.dispose();
}
* @author $author$
* @version $Revision$
*/
-public class AnnotationLabels extends JPanel implements MouseListener,
- MouseMotionListener, ActionListener
+public class AnnotationLabels extends JPanel
+ implements MouseListener, MouseMotionListener, ActionListener
{
private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern
.compile("<");
else if (evt.getActionCommand().equals(OUTPUT_TEXT))
{
new AnnotationExporter().exportAnnotations(ap,
- new AlignmentAnnotation[] { aa[selectedRow] });
+ new AlignmentAnnotation[]
+ { aa[selectedRow] });
}
else if (evt.getActionCommand().equals(COPYCONS_SEQ))
{
// av and sequencegroup need to implement same interface for
final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
MessageManager.getString("label.ignore_gaps_consensus"),
- (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
- .getIgnoreGapsConsensus() : ap.av
- .isIgnoreGapsConsensus());
+ (aa[selectedRow].groupRef != null)
+ ? aa[selectedRow].groupRef.getIgnoreGapsConsensus()
+ : ap.av.isIgnoreGapsConsensus());
final AlignmentAnnotation aaa = aa[selectedRow];
cbmi.addActionListener(new ActionListener()
{
{
// TODO: pass on reference to ap so the view can be updated.
aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
- ap.getAnnotationPanel().paint(
- ap.getAnnotationPanel().getGraphics());
+ ap.getAnnotationPanel()
+ .paint(ap.getAnnotationPanel().getGraphics());
}
else
{
if ((d.height - dif) > 20)
{
- ap.annotationScroller.setPreferredSize(new Dimension(d.width,
- d.height - dif));
+ ap.annotationScroller
+ .setPreferredSize(new Dimension(d.width, d.height - dif));
d = ap.annotationSpaceFillerHolder.getPreferredSize();
- ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
- d.width, d.height - dif));
+ ap.annotationSpaceFillerHolder
+ .setPreferredSize(new Dimension(d.width, d.height - dif));
ap.paintAlignment(true);
}
getSelectedRow(evt.getY() - getScrollOffset());
- if (selectedRow > -1
- && ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow)
+ if (selectedRow > -1 && ap.av.getAlignment()
+ .getAlignmentAnnotation().length > selectedRow)
{
AlignmentAnnotation aa = ap.av.getAlignment()
.getAlignmentAnnotation()[selectedRow];
// tooltips
desc.append(aa.getDescription(true).trim());
// check to see if the description is an html fragment.
- if (desc.length() < 6
- || (desc.substring(0, 6).toLowerCase().indexOf("<html>") < 0))
+ if (desc.length() < 6 || (desc.substring(0, 6).toLowerCase()
+ .indexOf("<html>") < 0))
{
// clean the description ready for embedding in html
desc = new StringBuffer(LEFT_ANGLE_BRACKET_PATTERN.matcher(desc)
ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
// process modifiers
SequenceGroup sg = ap.av.getSelectionGroup();
- if (sg == null
- || sg == aa[selectedRow].groupRef
- || !(jalview.util.Platform.isControlDown(evt) || evt
- .isShiftDown()))
+ if (sg == null || sg == aa[selectedRow].groupRef
+ || !(jalview.util.Platform.isControlDown(evt)
+ || evt.isShiftDown()))
{
if (jalview.util.Platform.isControlDown(evt)
|| evt.isShiftDown())
{
// clone a new selection group from the associated group
- ap.av.setSelectionGroup(new SequenceGroup(
- aa[selectedRow].groupRef));
+ ap.av.setSelectionGroup(
+ new SequenceGroup(aa[selectedRow].groupRef));
}
else
{
{
if (evt.getClickCount() == 1)
{
- ap.getSeqPanel().ap
- .getIdPanel()
- .highlightSearchResults(
- Arrays.asList(new SequenceI[] { aa[selectedRow].sequenceRef }));
+ ap.getSeqPanel().ap.getIdPanel()
+ .highlightSearchResults(Arrays.asList(new SequenceI[]
+ { aa[selectedRow].sequenceRef }));
}
else if (evt.getClickCount() >= 2)
{
// we make a copy rather than edit the current selection if no
// modifiers pressed
// see Enhancement JAL-1557
- if (!(jalview.util.Platform.isControlDown(evt) || evt
- .isShiftDown()))
+ if (!(jalview.util.Platform.isControlDown(evt)
+ || evt.isShiftDown()))
{
sg = new SequenceGroup(sg);
sg.clear();
if (av.hasHiddenColumns())
{
omitHidden = av.getAlignment().getHiddenColumns()
- .getVisibleSequenceStrings(0,
- sq.getLength(), seqs);
+ .getVisibleSequenceStrings(0, sq.getLength(), seqs);
}
int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 };
if (av.hasHiddenColumns())
{
alignmentStartEnd = av.getAlignment().getHiddenColumns()
- .getVisibleStartAndEndIndex(av.getAlignment().getWidth());
+ .getVisibleStartAndEndIndex(av.getAlignment().getWidth());
}
String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
int ofontH = fontHeight;
int sOffset = 0;
int visHeight = 0;
- int[] visr = (ap != null && ap.getAnnotationPanel() != null) ? ap
- .getAnnotationPanel().getVisibleVRange() : null;
+ int[] visr = (ap != null && ap.getAnnotationPanel() != null)
+ ? ap.getAnnotationPanel().getVisibleVRange()
+ : null;
if (clip && visr != null)
{
sOffset = visr[0];
{
if (debugRedraw)
{
- System.out.println("Scroll offset: " + sOffset
- + " after vis: " + i);
+ System.out.println(
+ "Scroll offset: " + sOffset + " after vis: " + i);
}
after = true;
}
}
if (groupSize * (fontHeight + 8) < aa[i].height)
{
- graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2;
+ graphExtras = (aa[i].height - (groupSize * (fontHeight + 8)))
+ / 2;
}
else
{
{
fontHeight = -8 + (int) h;
s = ((float) fontHeight) / (float) ofontH;
- Font f = baseFont.deriveFont(AffineTransform
- .getScaleInstance(s, s));
+ Font f = baseFont
+ .deriveFont(AffineTransform.getScaleInstance(s, s));
g.setFont(f);
fm = g.getFontMetrics();
- graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2;
+ graphExtras = (aa[i].height - (groupSize * (fontHeight + 8)))
+ / 2;
}
}
if (visible)
g.setColor(aa[gg]._linecolour);
g.drawLine(x, y - graphExtras + 3,
- x + fm.stringWidth(aa[gg].label), y - graphExtras
- + 3);
+ x + fm.stringWidth(aa[gg].label),
+ y - graphExtras + 3);
}
g.setColor(Color.black);
if (anot.length < av.getColumnSelection().getMax())
{
- Annotation[] temp = new Annotation[av.getColumnSelection().getMax() + 2];
+ Annotation[] temp = new Annotation[av.getColumnSelection().getMax()
+ + 2];
System.arraycopy(anot, 0, temp, 0, anot.length);
anot = temp;
aa[activeRow].annotations = anot;
anot[index] = new Annotation(label, "", type, 0);
}
- anot[index].secondaryStructure = type != 'S' ? type : label
- .length() == 0 ? ' ' : label.charAt(0);
+ anot[index].secondaryStructure = type != 'S' ? type
+ : label.length() == 0 ? ' ' : label.charAt(0);
anot[index].displayCharacter = label;
}
{
if (graphStretch > -1)
{
- av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY
- - evt.getY();
- if (av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight < 0)
+ av.getAlignment()
+ .getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY
+ - evt.getY();
+ if (av.getAlignment()
+ .getAlignmentAnnotation()[graphStretch].graphHeight < 0)
{
- av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight = 0;
+ av.getAlignment()
+ .getAlignmentAnnotation()[graphStretch].graphHeight = 0;
}
graphStretchY = evt.getY();
adjustPanelHeight();
int seqIndex = av.getAlignment().findIndex(seqref);
if (seqIndex != -1)
{
- text.append(", ")
- .append(MessageManager.getString("label.sequence"))
+ text.append(", ").append(MessageManager.getString("label.sequence"))
.append(" ").append(seqIndex + 1);
char residue = seqref.getCharAt(column);
if (!Comparison.isGap(residue))
String name;
if (av.getAlignment().isNucleotide())
{
- name = ResidueProperties.nucleotideName.get(String
- .valueOf(residue));
- text.append(" Nucleotide: ").append(
- name != null ? name : residue);
+ name = ResidueProperties.nucleotideName
+ .get(String.valueOf(residue));
+ text.append(" Nucleotide: ")
+ .append(name != null ? name : residue);
}
else
{
- name = 'X' == residue ? "X" : ('*' == residue ? "STOP"
- : ResidueProperties.aa2Triplet.get(String
- .valueOf(residue)));
+ name = 'X' == residue ? "X"
+ : ('*' == residue ? "STOP"
+ : ResidueProperties.aa2Triplet
+ .get(String.valueOf(residue)));
text.append(" Residue: ").append(name != null ? name : residue);
}
int residuePos = seqref.findPosition(column);
return;
}
}
- imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes() + 1)
- * av.getCharWidth();
+ imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes()
+ + 1) * av.getCharWidth();
if (imgWidth < 1)
{
return;
{
try
{
- image = new BufferedImage(imgWidth, ap.getAnnotationPanel()
- .getHeight(), BufferedImage.TYPE_INT_RGB);
+ image = new BufferedImage(imgWidth,
+ ap.getAnnotationPanel().getHeight(),
+ BufferedImage.TYPE_INT_RGB);
} catch (OutOfMemoryError oom)
{
try
imageFresh = true;
}
- drawComponent(gg, av.getRanges().getStartRes(), av.getRanges()
- .getEndRes() + 1);
+ drawComponent(gg, av.getRanges().getStartRes(),
+ av.getRanges().getEndRes() + 1);
imageFresh = false;
g.drawImage(image, 0, 0, this);
}
// and draw a faded image until the calculation
// has completed
if (lastImageGood
- && (fadedImage == null || fadedImage.getWidth() != imgWidth || fadedImage
- .getHeight() != image.getHeight()))
+ && (fadedImage == null || fadedImage.getWidth() != imgWidth
+ || fadedImage.getHeight() != image.getHeight()))
{
// System.err.println("redraw faded image ("+(fadedImage==null ?
// "null image" : "") + " lastGood="+lastImageGood+")");
fadedG.setColor(Color.white);
fadedG.fillRect(0, 0, imgWidth, image.getHeight());
- fadedG.setComposite(AlphaComposite.getInstance(
- AlphaComposite.SRC_OVER, .3f));
+ fadedG.setComposite(
+ AlphaComposite.getInstance(AlphaComposite.SRC_OVER, .3f));
fadedG.drawImage(image, 0, 0, this);
}
return;
}
- lastImageGood = renderer.drawComponent(this, av, g, activeRow,
- startRes, endRes);
+ lastImageGood = renderer.drawComponent(this, av, g, activeRow, startRes,
+ endRes);
if (!lastImageGood && fadedImage == null)
{
fadedImage = oldFaded;
* @param viewport
* @param alignPanel
*/
- public AnnotationRowFilter(AlignViewport viewport, final AlignmentPanel alignPanel)
+ public AnnotationRowFilter(AlignViewport viewport,
+ final AlignmentPanel alignPanel)
{
this.av = viewport;
this.ap = alignPanel;
}
adjusting = oldadj;
}
+
protected void addSliderMouseListeners()
{
});
}
-/**
- * Builds and returns a list of menu items (display text) for choice of
- * annotation. Also builds maps between annotations, their positions in the
- * list, and their display labels in the list.
- *
- * @param isSeqAssociated
- * @return
- */
+ /**
+ * Builds and returns a list of menu items (display text) for choice of
+ * annotation. Also builds maps between annotations, their positions in the
+ * list, and their display labels in the list.
+ *
+ * @param isSeqAssociated
+ * @return
+ */
public Vector<String> getAnnotationItems(boolean isSeqAssociated)
{
annotationLabels = new HashMap<AlignmentAnnotation, String>();
Vector<String> list = new Vector<String>();
int index = 1;
- int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
+ int[] anmap = new int[av.getAlignment()
+ .getAlignmentAnnotation().length];
seqAssociated.setEnabled(false);
- for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+ for (int i = 0; i < av.getAlignment()
+ .getAlignmentAnnotation().length; i++)
{
AlignmentAnnotation annotation = av.getAlignment()
.getAlignmentAnnotation()[i];
float f = Float.parseFloat(thresholdValue.getText());
if (percentThreshold.isSelected())
{
- slider.setValue(slider.getMinimum()
- + ((int) ((f / 100f) * (slider.getMaximum() - slider
- .getMinimum()))));
+ slider.setValue(slider.getMinimum() + ((int) ((f / 100f)
+ * (slider.getMaximum() - slider.getMinimum()))));
}
else
{
}
float thr = annotation.threshold.value;
- for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+ for (int i = 0; i < av.getAlignment()
+ .getAlignmentAnnotation().length; i++)
{
- AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[i];
+ AlignmentAnnotation aa = av.getAlignment()
+ .getAlignmentAnnotation()[i];
if (aa.label.equals(annotation.label)
&& (annotation.getCalcId() == null ? aa.getCalcId() == null
: annotation.getCalcId().equals(aa.getCalcId())))
selectedAnnotationChanged();
}
});
- annotations.setToolTipText(MessageManager
- .getString("info.select_annotation_row"));
+ annotations.setToolTipText(
+ MessageManager.getString("info.select_annotation_row"));
threshold.addActionListener(new ActionListener()
{
}
});
- percentThreshold.setText(MessageManager.getString("label.as_percentage"));
+ percentThreshold
+ .setText(MessageManager.getString("label.as_percentage"));
percentThreshold.addActionListener(new ActionListener()
{
@Override
*/
public AppJmol(String[] files, String[] ids, SequenceI[][] seqs,
AlignmentPanel ap, boolean usetoColour, boolean useToAlign,
- boolean leaveColouringToJmol, String loadStatus,
- Rectangle bounds, String viewid)
+ boolean leaveColouringToJmol, String loadStatus, Rectangle bounds,
+ String viewid)
{
PDBEntry[] pdbentrys = new PDBEntry[files.length];
for (int i = 0; i < pdbentrys.length; i++)
this.addInternalFrameListener(new InternalFrameAdapter()
{
@Override
- public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
+ public void internalFrameClosing(
+ InternalFrameEvent internalFrameEvent)
{
closeViewer(false);
}
this.addInternalFrameListener(new InternalFrameAdapter()
{
@Override
- public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
+ public void internalFrameClosing(
+ InternalFrameEvent internalFrameEvent)
{
closeViewer(false);
}
scriptWindow.setVisible(false);
}
- jmb.allocateViewer(renderPanel, true, "", null, null, "",
- scriptWindow, null);
+ jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow,
+ null);
// jmb.newJmolPopup("Jmol");
if (command == null)
{
jmb.setFinishedInit(true);
}
-
-
boolean allChainsSelected = false;
@Override
int waitFor = 35;
int waitTotal = 0;
while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
- : !(jmb.isFinishedInit() && jmb.getStructureFiles() != null && jmb
- .getStructureFiles().length == files.size()))
+ : !(jmb.isFinishedInit() && jmb.getStructureFiles() != null
+ && jmb.getStructureFiles().length == files.size()))
{
try
{
}
if (waitTotal > waitMax)
{
- System.err
- .println("Timed out waiting for Jmol to load files after "
- + waitTotal + "ms");
-// System.err.println("finished: " + jmb.isFinishedInit()
-// + "; loaded: " + Arrays.toString(jmb.getPdbFile())
-// + "; files: " + files.toString());
+ System.err.println("Timed out waiting for Jmol to load files after "
+ + waitTotal + "ms");
+ // System.err.println("finished: " + jmb.isFinishedInit()
+ // + "; loaded: " + Arrays.toString(jmb.getPdbFile())
+ // + "; files: " + files.toString());
jmb.getStructureFiles();
break;
}
long hdl = pdbid.hashCode() - System.currentTimeMillis();
if (progressBar != null)
{
- progressBar.setProgressBar(MessageManager.formatMessage(
- "status.fetching_pdb", new String[] { pdbid }), hdl);
+ progressBar.setProgressBar(MessageManager
+ .formatMessage("status.fetching_pdb", new String[]
+ { pdbid }), hdl);
}
try
{
}
if (errormsgs.length() > 0)
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
- .formatMessage("label.pdb_entries_couldnt_be_retrieved",
- new String[] { errormsgs.toString() }),
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.pdb_entries_couldnt_be_retrieved", new String[]
+ { errormsgs.toString() }),
MessageManager.getString("label.couldnt_load_file"),
JvOptionPane.ERROR_MESSAGE);
}
if (e == jmb.getPdbCount() - 1 || sb.length() > 20)
{
lines++;
- g.drawString(sb.toString(), 20, currentSize.height / 2 - lines
- * g.getFontMetrics().getHeight());
+ g.drawString(sb.toString(), 20, currentSize.height / 2
+ - lines * g.getFontMetrics().getHeight());
}
}
}
private AppJmol appJmolWindow;
public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
- PDBEntry[] pdbentry, SequenceI[][] sequenceIs, DataSourceType protocol)
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
+ DataSourceType protocol)
{
super(sSm, pdbentry, sequenceIs, protocol);
appJmolWindow = appJmol;
public jalview.api.FeatureRenderer getFeatureRenderer(
AlignmentViewPanel alignment)
{
- AlignmentPanel ap = (alignment == null) ? appJmolWindow
- .getAlignmentPanel() : (AlignmentPanel) alignment;
+ AlignmentPanel ap = (alignment == null)
+ ? appJmolWindow.getAlignmentPanel()
+ : (AlignmentPanel) alignment;
if (ap.av.isShowSequenceFeatures())
{
return ap.av.getAlignPanel().getSeqPanel().seqCanvas.fr;
import fr.orsay.lri.varna.models.rna.ModeleBase;
import fr.orsay.lri.varna.models.rna.RNA;
-public class AppVarna extends JInternalFrame implements SelectionListener,
- SecondaryStructureListener, InterfaceVARNASelectionListener,
- VamsasSource
+public class AppVarna extends JInternalFrame
+ implements SelectionListener, SecondaryStructureListener,
+ InterfaceVARNASelectionListener, VamsasSource
{
private static final byte[] PAIRS = new byte[] { '(', ')', '[', ']', '{',
'}', '<', '>' };
{
this(ap);
- String sname = aa.sequenceRef == null ? "secondary structure (alignment)"
+ String sname = aa.sequenceRef == null
+ ? "secondary structure (alignment)"
: seq.getName() + " structure";
String theTitle = sname
- + (aa.sequenceRef == null ? " trimmed to " + seq.getName() : "");
+ + (aa.sequenceRef == null ? " trimmed to " + seq.getName()
+ : "");
theTitle = MessageManager.formatMessage("label.varna_params",
- new String[] { theTitle });
+ new String[]
+ { theTitle });
setTitle(theTitle);
String gappedTitle = sname + " (with gaps)";
addModel(gappedModel, gappedTitle);
String trimmedTitle = "trimmed " + sname;
- RnaModel trimmedModel = new RnaModel(trimmedTitle, aa, seq, null, false);
+ RnaModel trimmedModel = new RnaModel(trimmedTitle, aa, seq, null,
+ false);
addModel(trimmedModel, trimmedTitle);
vab.setSelectedIndex(0);
}
end = shift.shift(end);
}
selectionHighlighter.highlightRegion(rna, start, end);
- selectionHighlighter.getLastHighlight().setOutlineColor(
- seqsel.getOutlineColour());
+ selectionHighlighter.getLastHighlight()
+ .setOutlineColor(seqsel.getOutlineColour());
// TODO - translate column markings to positions on structure if present.
vab.updateSelectedRNA(rna);
}
}
@Override
- public void onSelectionChanged(BaseList arg0, BaseList arg1, BaseList arg2)
+ public void onSelectionChanged(BaseList arg0, BaseList arg1,
+ BaseList arg2)
{
// TODO translate selected regions in VARNA to a selection on the
// alignpanel.
{
if (!model.ann.isValidStruc())
{
- throw new IllegalArgumentException("Invalid RNA structure annotation");
+ throw new IllegalArgumentException(
+ "Invalid RNA structure annotation");
}
/*
{
if (!model.ann.isValidStruc())
{
- throw new IllegalArgumentException("Invalid RNA structure annotation");
+ throw new IllegalArgumentException(
+ "Invalid RNA structure annotation");
}
try
String name = r.getName();
if (name.equals(""))
{
- name = path.substring(path
- .lastIndexOf(File.separatorChar) + 1);
+ name = path.substring(
+ path.lastIndexOf(File.separatorChar) + 1);
}
if (mdls.size() > 1)
{
PDBEntry entry = new PDBEntry();
StructureFile pdbfile = null;
pdbfile = StructureSelectionManager.getStructureSelectionManager(ssmp)
- .setMapping(false, new SequenceI[] { sequence }, null, choice,
- file);
+ .setMapping(false, new SequenceI[]
+ { sequence }, null, choice, file);
if (pdbfile == null)
{
// stacktrace already thrown so just return
_channelModel = new ChannelListModel();
// Construct our jalview news channel
Channel chan = new Channel();
- chan.setURL(jalview.bin.Cache.getDefault(
- "JALVIEW_NEWS_RSS",
- jalview.bin.Cache.getDefault("www.jalview.org",
- "http://www.jalview.org") + "/feeds/desktop/rss"));
+ chan.setURL(
+ jalview.bin.Cache.getDefault("JALVIEW_NEWS_RSS",
+ jalview.bin.Cache.getDefault("www.jalview.org",
+ "http://www.jalview.org")
+ + "/feeds/desktop/rss"));
loadLastM();
_channelModel.addChannel(chan);
updating = true;
public void windowClosing(WindowEvent e)
{
ActionEvent actionEvent = new ActionEvent(this,
- ActionEvent.ACTION_FIRST, (String) exitAction
- .getValue(Action.NAME));
+ ActionEvent.ACTION_FIRST,
+ (String) exitAction.getValue(Action.NAME));
exitAction.actionPerformed(actionEvent);
}
java.util.Date earliest = null;
try
{
- earliest = new SimpleDateFormat("YYYY-MM-DD").parse(chan
- .getHTTPLastModified());
+ earliest = new SimpleDateFormat("YYYY-MM-DD")
+ .parse(chan.getHTTPLastModified());
} catch (Exception x)
{
}
}
if (lastDate != null)
{
- String formatted = Cache.setDateProperty(
- "JALVIEW_NEWS_RSS_LASTMODIFIED", lastDate);
+ String formatted = Cache
+ .setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", lastDate);
Cache.log.debug("Saved last read date as " + formatted);
}
}
_itemsValueChanged(listItems);
}
- public class LaunchJvBrowserOnItem extends AbstractAction implements
- UpdatableAction
+ public class LaunchJvBrowserOnItem extends AbstractAction
+ implements UpdatableAction
{
JList _listItems = null;
private JPopupMenu _buildChannelsPopupMenu()
{
JPopupMenu popup = new JPopupMenu();
- popup.add(new JMenuItem(new MarkChannelAsRead(listChannels, listItems)));
+ popup.add(
+ new JMenuItem(new MarkChannelAsRead(listChannels, listItems)));
popup.add(new JMenuItem(
new MarkChannelAsUnread(listChannels, listItems)));
return popup;
}
DefaultListModel itemsModel = (DefaultListModel) listItems.getModel();
itemsModel.clear();
- Iterator iter = (channel.getItems() != null) ? channel.getItems()
- .iterator() : Collections.EMPTY_LIST.iterator();
+ Iterator iter = (channel.getItems() != null)
+ ? channel.getItems().iterator()
+ : Collections.EMPTY_LIST.iterator();
while (iter.hasNext())
{
itemsModel.addElement(iter.next());
button.setVerticalTextPosition(AbstractButton.BOTTOM);
button.setHorizontalTextPosition(AbstractButton.CENTER);
}
- else if (Boolean.toString(true).equals(
- general.get("radioTextRight")))
+ else if (Boolean.toString(true)
+ .equals(general.get("radioTextRight")))
{
button.setVerticalTextPosition(AbstractButton.CENTER);
button.setHorizontalTextPosition(AbstractButton.RIGHT);
jalview.bin.Cache.loadProperties(null);
jalview.bin.Cache.initLogger();
// test will advance read date each time
- Calendar today = Calendar.getInstance(), lastread = Calendar
- .getInstance();
+ Calendar today = Calendar.getInstance(),
+ lastread = Calendar.getInstance();
lastread.set(1983, 01, 01);
while (lastread.before(today))
{
if (value instanceof Channel)
{
Channel channel = (Channel) value;
- component
- .setText(MessageManager.formatMessage(
- "label.channel_title_item_count",
- new String[] {
- channel.getTitle(),
- Integer.valueOf(channel.getUnreadItemCount())
- .toString() }));
+ component.setText(MessageManager
+ .formatMessage("label.channel_title_item_count", new String[]
+ { channel.getTitle(), Integer
+ .valueOf(channel.getUnreadItemCount()).toString() }));
component.setToolTipText(channel.getURL());
}
return component;
if (item.getPublishDate() != null)
{
component.setText(MessageManager.formatMessage(
- "label.blog_item_published_on_date",
- new String[] {
- DateFormat
- .getDateInstance(DateFormat.LONG,
- MessageManager.getLocale())
- .format(item.getPublishDate()).toString(),
+ "label.blog_item_published_on_date", new String[]
+ { DateFormat
+ .getDateInstance(DateFormat.LONG,
+ MessageManager.getLocale())
+ .format(item.getPublishDate()).toString(),
item.getTitle() }));
}
component.setToolTipText(item.getLink());
JPanel treePanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
treePanel.setOpaque(false);
- treePanel.setBorder(BorderFactory.createTitledBorder(MessageManager
- .getString("label.tree")));
+ treePanel.setBorder(BorderFactory
+ .createTitledBorder(MessageManager.getString("label.tree")));
// then copy the inset dimensions for the border-less PCA panel
JPanel pcaBorderless = new JPanel(new FlowLayout(FlowLayout.LEFT));
Insets b = treePanel.getBorder().getBorderInsets(treePanel);
- pcaBorderless.setBorder(BorderFactory.createEmptyBorder(2, b.left, 2,
- b.right));
+ pcaBorderless.setBorder(
+ BorderFactory.createEmptyBorder(2, b.left, 2, b.right));
pcaBorderless.setOpaque(false);
pcaBorderless.add(pca, FlowLayout.LEFT);
calcTypes.add(pca);
calcTypes.add(neighbourJoining);
calcTypes.add(averageDistance);
-
+
ActionListener calcChanged = new ActionListener()
{
@Override
*/
private boolean checkEnabled(JRadioButton calc, int size, int minsize)
{
- String ttip = MessageManager.formatMessage(
- "label.you_need_at_least_n_sequences", minsize);
+ String ttip = MessageManager
+ .formatMessage("label.you_need_at_least_n_sequences", minsize);
calc.setEnabled(size >= minsize);
if (!calc.isEnabled())
@Override
public void mouseEntered(MouseEvent e)
{
- scoreModelsCombo.setToolTipText(tips.get(scoreModelsCombo.getSelectedIndex()));
+ scoreModelsCombo.setToolTipText(
+ tips.get(scoreModelsCombo.getSelectedIndex()));
}
@Override
SequenceGroup sg = viewport.getSelectionGroup();
if (sg != null && sg.getSize() < MIN_TREE_SELECTION)
{
- JvOptionPane
- .showMessageDialog(
- Desktop.desktop,
- MessageManager
- .formatMessage("label.you_need_at_least_n_sequences",
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.you_need_at_least_n_sequences",
MIN_TREE_SELECTION),
- MessageManager
- .getString("label.not_enough_sequences"),
- JvOptionPane.WARNING_MESSAGE);
+ MessageManager.getString("label.not_enough_sequences"),
+ JvOptionPane.WARNING_MESSAGE);
return;
}
- String treeType = neighbourJoining.isSelected() ? TreeBuilder.NEIGHBOUR_JOINING
+ String treeType = neighbourJoining.isSelected()
+ ? TreeBuilder.NEIGHBOUR_JOINING
: TreeBuilder.AVERAGE_DISTANCE;
af.newTreePanel(treeType, modelName, params);
}
* this check in in case this method gets exposed programmatically in future
*/
if (((viewport.getSelectionGroup() != null)
- && (viewport.getSelectionGroup().getSize() < MIN_PCA_SELECTION) && (viewport
- .getSelectionGroup().getSize() > 0))
+ && (viewport.getSelectionGroup().getSize() < MIN_PCA_SELECTION)
+ && (viewport.getSelectionGroup().getSize() > 0))
|| (viewport.getAlignment().getHeight() < MIN_PCA_SELECTION))
{
- JvOptionPane.showInternalMessageDialog(this, MessageManager
- .formatMessage("label.you_need_at_least_n_sequences",
- MIN_PCA_SELECTION), MessageManager
- .getString("label.sequence_selection_insufficient"),
+ JvOptionPane.showInternalMessageDialog(this,
+ MessageManager.formatMessage(
+ "label.you_need_at_least_n_sequences",
+ MIN_PCA_SELECTION),
+ MessageManager
+ .getString("label.sequence_selection_insufficient"),
JvOptionPane.WARNING_MESSAGE);
return;
}
*/
boolean matchGap = doPCA ? false : treeMatchGaps;
- return new SimilarityParams(includeGapGap, matchGap, includeGapResidue, matchOnShortestLength);
+ return new SimilarityParams(includeGapGap, matchGap, includeGapResidue,
+ matchOnShortestLength);
}
/**
viewerActionMenu.setText(MessageManager.getString("label.chimera"));
- viewerColour.setText(MessageManager
- .getString("label.colour_with_chimera"));
+ viewerColour
+ .setText(MessageManager.getString("label.colour_with_chimera"));
viewerColour.setToolTipText(MessageManager
.getString("label.let_chimera_manage_structure_colours"));
protected void sendFeaturesToChimera()
{
int count = jmb.sendFeaturesToViewer(getAlignmentPanel());
- statusBar.setText(MessageManager.formatMessage("label.attributes_set",
- count));
+ statusBar.setText(
+ MessageManager.formatMessage("label.attributes_set", count));
}
/**
* a new viewer
*/
openNewChimera(ap, new PDBEntry[] { pdbentry },
- new SequenceI[][] { seq });
+ new SequenceI[][]
+ { seq });
}
/**
this.addInternalFrameListener(new InternalFrameAdapter()
{
@Override
- public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
+ public void internalFrameClosing(
+ InternalFrameEvent internalFrameEvent)
{
closeViewer(false);
}
boolean opened = jmb.openSession(chimeraSessionFile);
if (!opened)
{
- System.err
- .println("An error occurred opening Chimera session file "
- + chimeraSessionFile);
+ System.err.println("An error occurred opening Chimera session file "
+ + chimeraSessionFile);
}
}
{
if (!closeChimera)
{
- String prompt = MessageManager.formatMessage(
- "label.confirm_close_chimera",
- new Object[] { jmb.getViewerTitle(getViewerName(),
- false) });
+ String prompt = MessageManager
+ .formatMessage("label.confirm_close_chimera", new Object[]
+ { jmb.getViewerTitle(getViewerName(), false) });
prompt = JvSwingUtils.wrapTooltip(true, prompt);
int confirm = JvOptionPane.showConfirmDialog(this, prompt,
MessageManager.getString("label.close_viewer"),
} catch (Exception ex)
{
ex.printStackTrace();
- errormsgs.append("When retrieving pdbfiles for '"
- + thePdbEntry.getId() + "'");
+ errormsgs.append(
+ "When retrieving pdbfiles for '" + thePdbEntry.getId() + "'");
}
if (errormsgs.length() > 0)
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
- .formatMessage("label.pdb_entries_couldnt_be_retrieved",
- new Object[] { errormsgs.toString() }),
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.pdb_entries_couldnt_be_retrieved", new Object[]
+ { errormsgs.toString() }),
MessageManager.getString("label.couldnt_load_file"),
JvOptionPane.ERROR_MESSAGE);
}
oomerror);
} catch (Exception ex)
{
- Cache.log.error("Couldn't open " + pe.getFile()
- + " in Chimera viewer!", ex);
+ Cache.log.error(
+ "Couldn't open " + pe.getFile() + " in Chimera viewer!",
+ ex);
} finally
{
Cache.log.debug("File locations are " + files);
{
for (int i = 0; i < pdb.getChains().size(); i++)
{
- String chid = new String(pdb.getId() + ":"
- + pdb.getChains().elementAt(i).id);
+ String chid = new String(
+ pdb.getId() + ":" + pdb.getChains().elementAt(i).id);
jmb.getChainNames().add(chid);
jmb.getChainFile().put(chid, file);
}
}
+
private String fetchPdbFile(PDBEntry processingEntry) throws Exception
{
// FIXME: this is duplicated code with Jmol frame ?
* Write 'fetching PDB' progress on AlignFrame as we are not yet visible
*/
String msg = MessageManager.formatMessage("status.fetching_pdb",
- new Object[] { pdbid });
+ new Object[]
+ { pdbid });
getAlignmentPanel().alignFrame.setProgressBar(msg, handle);
// long hdl = startProgressBar(MessageManager.formatMessage(
// "status.fetching_pdb", new Object[]
@Override
public void eps_actionPerformed(ActionEvent e)
{
- throw new Error(
- MessageManager
- .getString("error.eps_generation_not_implemented"));
+ throw new Error(MessageManager
+ .getString("error.eps_generation_not_implemented"));
}
@Override
public void png_actionPerformed(ActionEvent e)
{
- throw new Error(
- MessageManager
- .getString("error.png_generation_not_implemented"));
+ throw new Error(MessageManager
+ .getString("error.png_generation_not_implemented"));
}
@Override
* the colour scheme (inspected in setColourSelected())
*/
final String name = scheme.getSchemeName();
- String label = MessageManager.getStringOrReturn("label.colourScheme_"
- + name.toLowerCase().replace(" ", "_"), name);
- final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(label);
+ String label = MessageManager.getStringOrReturn(
+ "label.colourScheme_" + name.toLowerCase().replace(" ", "_"),
+ name);
+ final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
+ label);
radioItem.setName(name);
radioItem.setEnabled(scheme.isApplicableTo(coll));
if (scheme instanceof UserColourScheme)
ActionListener al = radioItem.getActionListeners()[0];
radioItem.removeActionListener(al);
int option = JvOptionPane.showInternalConfirmDialog(
- Desktop.desktop, MessageManager
+ Desktop.desktop,
+ MessageManager
.getString("label.remove_from_default_list"),
MessageManager
.getString("label.remove_user_defined_colour"),
JvOptionPane.YES_NO_OPTION);
if (option == JvOptionPane.YES_OPTION)
{
- ColourSchemes.getInstance().removeColourScheme(
- radioItem.getName());
+ ColourSchemes.getInstance()
+ .removeColourScheme(radioItem.getName());
colourMenu.remove(radioItem);
updatePreferences();
}
@Override
public void actionPerformed(ActionEvent e)
{
- client.changeColour_actionPerformed(ResidueColourScheme.USER_DEFINED_MENU);
+ client.changeColour_actionPerformed(
+ ResidueColourScheme.USER_DEFINED_MENU);
}
});
colourMenu.add(userDefinedColour);
* Marks as selected the colour menu item matching the given colour scheme, or
* the first item ('None') if no match is found. If the colour scheme is a
* user defined scheme, but not in the menu (this arises if a new scheme is
- * defined and applied but not saved to file), then menu option
- * "User Defined.." is selected.
+ * defined and applied but not saved to file), then menu option "User
+ * Defined.." is selected.
*
* @param colourMenu
* @param cs
*/
public static void setColourSelected(JMenu colourMenu, ColourSchemeI cs)
{
- String colourName = cs == null ? ResidueColourScheme.NONE : cs
- .getSchemeName();
+ String colourName = cs == null ? ResidueColourScheme.NONE
+ : cs.getSchemeName();
JRadioButtonMenuItem none = null;
JRadioButtonMenuItem userDefined = null;
* own applications RJHM van den Bergh , rvdb@comweb.nl
*/
-public class Console extends WindowAdapter implements WindowListener,
- ActionListener, Runnable
+public class Console extends WindowAdapter
+ implements WindowListener, ActionListener, Runnable
{
private JFrame frame;
}
else
{
- frame = initFrame("Jalview Java Console", bounds.width,
- bounds.height, bounds.x, bounds.y);
+ frame = initFrame("Jalview Java Console", bounds.width, bounds.height,
+ bounds.x, bounds.y);
}
frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
// desktop.add(frame);
textArea.append("The error is: " + e.getMessage());
// Need to uncomment this to ensure that line tally is synched.
// lines += 2;
- stderr.println("Console reports an Internal error.\nThe error is: "
- + e);
+ stderr.println(
+ "Console reports an Internal error.\nThe error is: " + e);
}
// just for testing (Throw a Nullpointer after 1 second)
public void run()
{
final long sttime = System.currentTimeMillis();
- alignFrame.setProgressBar(
- MessageManager.formatMessage(
- "status.searching_for_sequences_from",
- new Object[] { source }), sttime);
+ alignFrame.setProgressBar(MessageManager.formatMessage(
+ "status.searching_for_sequences_from", new Object[]
+ { source }), sttime);
try
{
AlignmentI alignment = alignFrame.getViewport().getAlignment();
+ " now searching for " + (dna ? "DNA" : "Protein")
+ " Context.");
}
- AlignmentI xrefs = new CrossRef(sel, dataset).findXrefSequences(
- source, dna);
+ AlignmentI xrefs = new CrossRef(sel, dataset)
+ .findXrefSequences(source, dna);
if (xrefs == null)
{
return;
if (copyAlignment.getHeight() <= 0)
{
- System.err.println("No Sequences generated for xRef type "
- + source);
+ System.err.println(
+ "No Sequences generated for xRef type " + source);
return;
}
/*
} finally
{
alignFrame.setProgressBar(MessageManager.formatMessage(
- "status.finished_searching_for_sequences_from",
- new Object[] { source }), sttime);
+ "status.finished_searching_for_sequences_from", new Object[]
+ { source }), sttime);
}
}
for (int s = 0; s < sprods.length; s++)
{
sprods[s] = (seqs.getSequenceAt(s)).deriveSequence();
- if (dataset.getSequences() == null
- || !dataset.getSequences().contains(
- sprods[s].getDatasetSequence()))
+ if (dataset.getSequences() == null || !dataset.getSequences()
+ .contains(sprods[s].getDatasetSequence()))
{
dataset.addSequence(sprods[s].getDatasetSequence());
}
chooser.setAcceptAllFileFilterUsed(false);
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager
- .getString("label.save_text_to_file"));
+ chooser.setDialogTitle(
+ MessageManager.getString("label.save_text_to_file"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
public void toggleHtml_actionPerformed(ActionEvent e)
{
String txt = textarea.getText();
- textarea.setContentType(displaySource.isSelected() ? "text/text"
- : "text/html");
+ textarea.setContentType(
+ displaySource.isSelected() ? "text/text" : "text/html");
textarea.setText(txt);
}
chooser.setAcceptAllFileFilterUsed(false);
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager
- .getString("label.save_text_to_file"));
+ chooser.setDialogTitle(
+ MessageManager.getString("label.save_text_to_file"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
{
try
{
- PrintWriter out = new PrintWriter(new FileWriter(
- chooser.getSelectedFile()));
+ PrintWriter out = new PrintWriter(
+ new FileWriter(chooser.getSelectedFile()));
out.print(getText());
out.close();
try
{
- textarea.append((String) contents
- .getTransferData(DataFlavor.stringFlavor));
+ textarea.append(
+ (String) contents.getTransferData(DataFlavor.stringFlavor));
} catch (Exception ex)
{
}
}
if (format == null)
{
- System.err.println(MessageManager
- .getString("label.couldnt_read_data"));
+ System.err
+ .println(MessageManager.getString("label.couldnt_read_data"));
if (!Jalview.isHeadlessMode())
{
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
{
JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
.formatMessage("label.couldnt_read_pasted_text", new String[]
- { ex.toString() }), MessageManager
- .getString("label.error_parsing_text"),
+ { ex.toString() }),
+ MessageManager.getString("label.error_parsing_text"),
JvOptionPane.WARNING_MESSAGE);
}
if (al != null && al.hasValidSequence())
{
- String title = MessageManager.formatMessage(
- "label.input_cut_paste_params",
- new String[] { format.getName() });
+ String title = MessageManager
+ .formatMessage("label.input_cut_paste_params", new String[]
+ { format.getName() });
FeatureSettingsModelI proxyColourScheme = source
.getFeatureColourScheme();
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
af.getViewport().setShowSequenceFeatures(showSeqFeatures);
af.getViewport().setFeaturesDisplayed(fd);
- ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
- colourSchemeName, al);
+ ColourSchemeI cs = ColourSchemeMapper
+ .getJalviewColourScheme(colourSchemeName, al);
if (cs != null)
{
af.changeColour(cs);
try
{
- af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
- false));
+ af.setMaximum(
+ jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
} catch (Exception ex)
{
}
}
else
{
- System.err.println(MessageManager
- .getString("label.couldnt_read_data"));
+ System.err
+ .println(MessageManager.getString("label.couldnt_read_data"));
if (!Jalview.isHeadlessMode())
{
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
import org.biodas.jdas.schema.sources.PROP;
import org.biodas.jdas.schema.sources.VERSION;
-public class DasSourceBrowser extends GDasSourceBrowser implements
- Runnable, ListSelectionListener
+public class DasSourceBrowser extends GDasSourceBrowser
+ implements Runnable, ListSelectionListener
{
DasSourceRegistryI sourceRegistry = null;
for (int i = 0; i < dSize; i++)
{
data[i][0] = sources.get(i).getTitle(); // what's equivalent of nickname
- data[i][1] = new Boolean(selectedSources.contains(sources.get(i)
- .getTitle()));
+ data[i][1] = new Boolean(
+ selectedSources.contains(sources.get(i).getTitle()));
}
refreshTableData(data);
if (nickName == null)
{
- fullDetails.setText(text
- + MessageManager
- .getString("label.select_das_service_from_table"));
+ fullDetails.setText(text + MessageManager
+ .getString("label.select_das_service_from_table"));
return;
}
}
VERSION latest = ds.getVersion();
- text.append("<font color=\"#0000FF\">Id:</font> " + ds.getUri()
- + "<br>");
+ text.append(
+ "<font color=\"#0000FF\">Id:</font> " + ds.getUri() + "<br>");
text.append("<font color=\"#0000FF\">Nickname:</font> "
+ ds.getTitle() + "<br>");
text.append("<font color=\"#0000FF\">Description:</font> "
+ ds.getDescription() + "<br>");
- text.append("<font color=\"#0000FF\">Admin Email:</font> <a href=\"mailto:"
- + ds.getEmail() + "\">" + ds.getEmail() + "</a>" + "<br>");
+ text.append(
+ "<font color=\"#0000FF\">Admin Email:</font> <a href=\"mailto:"
+ + ds.getEmail() + "\">" + ds.getEmail() + "</a>"
+ + "<br>");
text.append("<font color=\"#0000FF\">Registered at:</font> "
+ latest.getCreated() + "<br>");
panel.add(pane12, BorderLayout.SOUTH);
int reply = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
- panel,
- MessageManager.getString("label.enter_local_das_source"),
+ panel, MessageManager.getString("label.enter_local_das_source"),
JvOptionPane.OK_CANCEL_OPTION);
if (reply != JvOptionPane.OK_OPTION)
urltf.setText(urltf.getText() + "/");
}
- jalviewSourceI local = sourceRegistry.createLocalSource(
- urltf.getText(), nametf.getText(), seqs.isSelected(), true);
+ jalviewSourceI local = sourceRegistry.createLocalSource(urltf.getText(),
+ nametf.getText(), seqs.isSelected(), true);
List sources = sourceRegistry.getSources();
int osize = sources.size();
int size = osize + (newSource ? 1 : 0);
Object[][] data = new Object[size][2];
- DASTableModel dtm = (table != null) ? (DASTableModel) ((TableSorter) table
- .getModel()).getTableModel() : null;
+ DASTableModel dtm = (table != null)
+ ? (DASTableModel) ((TableSorter) table.getModel())
+ .getTableModel()
+ : null;
for (int i = 0; i < osize; i++)
{
- String osrc = (dtm == null || i >= osize) ? null : (String) dtm
- .getValueAt(i, 0);
+ String osrc = (dtm == null || i >= osize) ? null
+ : (String) dtm.getValueAt(i, 0);
if (!newSource && osrc != null
&& dtm.getValueAt(i, 0).equals(nickname))
{
@Override
public void run()
{
- scrollPane.getVerticalScrollBar().setValue(
- scrollPane.getVerticalScrollBar().getMaximum());
+ scrollPane.getVerticalScrollBar()
+ .setValue(scrollPane.getVerticalScrollBar().getMaximum());
}
});
if (!sourceRegistry.getSource(nickname).isLocal())
{
- JvOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- MessageManager
- .getString("label.you_can_only_edit_or_remove_local_das_sources"),
- MessageManager.getString("label.public_das_source"),
- JvOptionPane.WARNING_MESSAGE);
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString(
+ "label.you_can_only_edit_or_remove_local_das_sources"),
+ MessageManager.getString("label.public_das_source"),
+ JvOptionPane.WARNING_MESSAGE);
return;
}
int choice = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
"Do you want to edit or remove " + nickname + "?",
"Edit / Remove Local DAS Source",
- JvOptionPane.YES_NO_CANCEL_OPTION, JvOptionPane.QUESTION_MESSAGE,
- null, options, options[2]);
+ JvOptionPane.YES_NO_CANCEL_OPTION,
+ JvOptionPane.QUESTION_MESSAGE, null, options, options[2]);
switch (choice)
{
sourceRegistry.removeLocalSource(sourceRegistry.getSource(nickname));
selectedSources.remove(nickname);
Object[][] data = new Object[sourceRegistry.getSources().size()][2];
- int index = 0,
- l = table.getRowCount();
+ int index = 0, l = table.getRowCount();
for (int i = 0; i < l; i++)
{
@Override
public void run()
{
- scrollPane.getVerticalScrollBar().setValue(
- scrollPane.getVerticalScrollBar().getMaximum());
+ scrollPane.getVerticalScrollBar()
+ .setValue(scrollPane.getVerticalScrollBar().getMaximum());
}
});
VERSION v = ds.getVersion();
List<COORDINATES> coords = v.getCOORDINATES();
- if (ds.isLocal()
- || ((coords == null || coords.size() == 0)
- && filter1.getSelectedIndex() == 0
- && filter2.getSelectedIndex() == 0 && filter3
- .getSelectedIndex() == 0))
+ if (ds.isLocal() || ((coords == null || coords.size() == 0)
+ && filter1.getSelectedIndex() == 0
+ && filter2.getSelectedIndex() == 0
+ && filter3.getSelectedIndex() == 0))
{
// THIS IS A FIX FOR LOCAL SOURCES WHICH DO NOT
// HAVE COORDINATE SYSTEMS, INFO WHICH AT PRESENT
for (int j = 0; j < coords.size(); j++)
{
if (selectedInList(filter1.getSelectedValues(),
- new String[] { coords.get(j).getAuthority() })
+ new String[]
+ { coords.get(j).getAuthority() })
&& selectedInList(filter2.getSelectedValues(), new String[]
{ coords.get(j).getSource() }))
{
names.add(ds.getTitle());
- selected.add(new Boolean(selectedSources.contains(ds.getTitle())));
+ selected.add(
+ new Boolean(selectedSources.contains(ds.getTitle())));
break;
}
}
* @author $author$
* @version $Revision: 1.155 $
*/
-public class Desktop extends jalview.jbgui.GDesktop implements
- DropTargetListener, ClipboardOwner, IProgressIndicator,
+public class Desktop extends jalview.jbgui.GDesktop
+ implements DropTargetListener, ClipboardOwner, IProgressIndicator,
jalview.api.StructureSelectionManagerProvider
{
private static int DEFAULT_MIN_WIDTH = 300;
setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE",
false);
- boolean showjconsole = jalview.bin.Cache.getDefault(
- "SHOW_JAVA_CONSOLE", false);
+ boolean showjconsole = jalview.bin.Cache.getDefault("SHOW_JAVA_CONSOLE",
+ false);
desktop = new MyDesktopPane(selmemusage);
if (Platform.isAMac())
{
// This line prevents Windows Look&Feel resizing all new windows to maximum
// if previous window was maximised
- desktop.setDesktopManager(new MyDesktopManager(
- new DefaultDesktopManager()));
+ desktop.setDesktopManager(
+ new MyDesktopManager(new DefaultDesktopManager()));
Rectangle dims = getLastKnownDimensions("");
if (dims != null)
else
{
Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
- setBounds((screenSize.width - 900) / 2,
- (screenSize.height - 650) / 2, 900, 650);
+ setBounds((screenSize.width - 900) / 2, (screenSize.height - 650) / 2,
+ 900, 650);
}
jconsole = new Console(this, showjconsole);
// add essential build information
- jconsole.setHeader("Jalview Version: "
- + jalview.bin.Cache.getProperty("VERSION") + "\n"
- + "Jalview Installation: "
- + jalview.bin.Cache.getDefault("INSTALLATION", "unknown")
- + "\n" + "Build Date: "
- + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown") + "\n"
- + "Java version: " + System.getProperty("java.version") + "\n"
- + System.getProperty("os.arch") + " "
- + System.getProperty("os.name") + " "
- + System.getProperty("os.version"));
+ jconsole.setHeader(
+ "Jalview Version: " + jalview.bin.Cache.getProperty("VERSION")
+ + "\n" + "Jalview Installation: "
+ + jalview.bin.Cache.getDefault("INSTALLATION",
+ "unknown")
+ + "\n" + "Build Date: "
+ + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
+ + "\n" + "Java version: "
+ + System.getProperty("java.version") + "\n"
+ + System.getProperty("os.arch") + " "
+ + System.getProperty("os.name") + " "
+ + System.getProperty("os.version"));
showConsole(showjconsole);
showNews.setVisible(false);
-
+
experimentalFeatures.setSelected(showExperimental());
getIdentifiersOrgData();
.getStructureSelectionManager(this);
if (jalview.bin.Cache.getDefault(Preferences.ADD_SS_ANN, true))
{
- ssm.setAddTempFacAnnot(jalview.bin.Cache.getDefault(
- Preferences.ADD_TEMPFACT_ANN, true));
- ssm.setProcessSecondaryStructure(jalview.bin.Cache.getDefault(
- Preferences.STRUCT_FROM_PDB, true));
- ssm.setSecStructServices(jalview.bin.Cache.getDefault(
- Preferences.USE_RNAVIEW, true));
+ ssm.setAddTempFacAnnot(jalview.bin.Cache
+ .getDefault(Preferences.ADD_TEMPFACT_ANN, true));
+ ssm.setProcessSecondaryStructure(jalview.bin.Cache
+ .getDefault(Preferences.STRUCT_FROM_PDB, true));
+ ssm.setSecStructServices(
+ jalview.bin.Cache.getDefault(Preferences.USE_RNAVIEW, true));
}
else
{
{
long now = System.currentTimeMillis();
Desktop.instance.setProgressBar(
- MessageManager.getString("status.refreshing_news"), now);
+ MessageManager.getString("status.refreshing_news"),
+ now);
jvnews.refreshNews();
Desktop.instance.setProgressBar(null, now);
jvnews.showNews();
Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
String x = jalview.bin.Cache.getProperty(windowName + "SCREEN_X");
String y = jalview.bin.Cache.getProperty(windowName + "SCREEN_Y");
- String width = jalview.bin.Cache.getProperty(windowName
- + "SCREEN_WIDTH");
- String height = jalview.bin.Cache.getProperty(windowName
- + "SCREEN_HEIGHT");
+ String width = jalview.bin.Cache
+ .getProperty(windowName + "SCREEN_WIDTH");
+ String height = jalview.bin.Cache
+ .getProperty(windowName + "SCREEN_HEIGHT");
if ((x != null) && (y != null) && (width != null) && (height != null))
{
- int ix = Integer.parseInt(x), iy = Integer.parseInt(y), iw = Integer
- .parseInt(width), ih = Integer.parseInt(height);
+ int ix = Integer.parseInt(x), iy = Integer.parseInt(y),
+ iw = Integer.parseInt(width), ih = Integer.parseInt(height);
if (jalview.bin.Cache.getProperty("SCREENGEOMETRY_WIDTH") != null)
{
// attempt #1 - try to cope with change in screen geometry - this
// version doesn't preserve original jv aspect ratio.
// take ratio of current screen size vs original screen size.
- double sw = ((1f * screenSize.width) / (1f * Integer
- .parseInt(jalview.bin.Cache
- .getProperty("SCREENGEOMETRY_WIDTH"))));
- double sh = ((1f * screenSize.height) / (1f * Integer
- .parseInt(jalview.bin.Cache
- .getProperty("SCREENGEOMETRY_HEIGHT"))));
+ double sw = ((1f * screenSize.width) / (1f * Integer.parseInt(
+ jalview.bin.Cache.getProperty("SCREENGEOMETRY_WIDTH"))));
+ double sh = ((1f * screenSize.height) / (1f * Integer.parseInt(
+ jalview.bin.Cache.getProperty("SCREENGEOMETRY_HEIGHT"))));
// rescale the bounds depending upon the current screen geometry.
ix = (int) (ix * sw);
iw = (int) (iw * sw);
ih = (int) (ih * sh);
while (ix >= screenSize.width)
{
- jalview.bin.Cache.log
- .debug("Window geometry location recall error: shifting horizontal to within screenbounds.");
+ jalview.bin.Cache.log.debug(
+ "Window geometry location recall error: shifting horizontal to within screenbounds.");
ix -= screenSize.width;
}
while (iy >= screenSize.height)
{
- jalview.bin.Cache.log
- .debug("Window geometry location recall error: shifting vertical to within screenbounds.");
+ jalview.bin.Cache.log.debug(
+ "Window geometry location recall error: shifting vertical to within screenbounds.");
iy -= screenSize.height;
}
- jalview.bin.Cache.log.debug("Got last known dimensions for "
- + windowName + ": x:" + ix + " y:" + iy + " width:" + iw
- + " height:" + ih);
+ jalview.bin.Cache.log.debug(
+ "Got last known dimensions for " + windowName + ": x:" + ix
+ + " y:" + iy + " width:" + iw + " height:" + ih);
}
// return dimensions for new instance
return new Rectangle(ix, iy, iw, ih);
}
} catch (Exception ex)
{
- System.out
- .println("Unable to paste alignment from system clipboard:\n"
- + ex);
+ System.out.println(
+ "Unable to paste alignment from system clipboard:\n" + ex);
}
}
// A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN
// IF JALVIEW IS RUNNING HEADLESS
// ///////////////////////////////////////////////
- if (instance == null
- || (System.getProperty("java.awt.headless") != null && System
- .getProperty("java.awt.headless").equals("true")))
+ if (instance == null || (System.getProperty("java.awt.headless") != null
+ && System.getProperty("java.awt.headless").equals("true")))
{
return;
}
if (!ignoreMinSize)
{
- frame.setMinimumSize(new Dimension(DEFAULT_MIN_WIDTH,
- DEFAULT_MIN_HEIGHT));
+ frame.setMinimumSize(
+ new Dimension(DEFAULT_MIN_WIDTH, DEFAULT_MIN_HEIGHT));
// Set default dimension for Alignment Frame window.
// The Alignment Frame window could be added from a number of places,
}
}
-
frame.setVisible(makeVisible);
frame.setClosable(true);
frame.setResizable(resizable);
}
if (frame.getX() < 1 && frame.getY() < 1)
{
- frame.setLocation(xOffset * openFrameCount, yOffset
- * ((openFrameCount - 1) % 10) + yOffset);
+ frame.setLocation(xOffset * openFrameCount,
+ yOffset * ((openFrameCount - 1) % 10) + yOffset);
}
/*
{
} catch (java.lang.ClassCastException cex)
{
- Cache.log
- .warn("Squashed a possible GUI implementation error. If you can recreate this, please look at http://issues.jalview.org/browse/JAL-869",
- cex);
+ Cache.log.warn(
+ "Squashed a possible GUI implementation error. If you can recreate this, please look at http://issues.jalview.org/browse/JAL-869",
+ cex);
}
}
for (int i = 0; i < files.size(); i++)
{
String file = files.get(i).toString();
- DataSourceType protocol = (protocols == null) ? DataSourceType.FILE
+ DataSourceType protocol = (protocols == null)
+ ? DataSourceType.FILE
: protocols.get(i);
FileFormatI format = null;
public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
{
String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
- JalviewFileChooser chooser = JalviewFileChooser.forRead(
- Cache.getProperty("LAST_DIRECTORY"), fileFormat);
+ JalviewFileChooser chooser = JalviewFileChooser
+ .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager
- .getString("label.open_local_file"));
+ chooser.setDialogTitle(
+ MessageManager.getString("label.open_local_file"));
chooser.setToolTipText(MessageManager.getString("action.open"));
int value = chooser.showOpenDialog(this);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
String choice = chooser.getSelectedFile().getPath();
- Cache.setProperty("LAST_DIRECTORY", chooser
- .getSelectedFile().getParent());
+ Cache.setProperty("LAST_DIRECTORY",
+ chooser.getSelectedFile().getParent());
FileFormatI format = chooser.getSelectedFormat();
{
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.formatMessage("label.couldnt_locate",
- new Object[] { url }), MessageManager
- .getString("label.url_not_found"),
+ new Object[]
+ { url }),
+ MessageManager.getString("label.url_not_found"),
JvOptionPane.WARNING_MESSAGE);
return;
if (viewport != null)
{
- new FileLoader()
- .LoadFile(viewport, url, DataSourceType.URL, format);
+ new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
+ format);
}
else
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(viewPanel);
Desktop.addInternalFrame(cap,
- MessageManager.getString("label.cut_paste_alignmen_file"),
- true, 600, 500);
+ MessageManager.getString("label.cut_paste_alignmen_file"), true,
+ 600, 500);
}
/*
public void quit()
{
Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
- jalview.bin.Cache
- .setProperty("SCREENGEOMETRY_WIDTH", screen.width + "");
- jalview.bin.Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height
- + "");
- storeLastKnownDimensions("", new Rectangle(getBounds().x,
- getBounds().y, getWidth(), getHeight()));
+ jalview.bin.Cache.setProperty("SCREENGEOMETRY_WIDTH",
+ screen.width + "");
+ jalview.bin.Cache.setProperty("SCREENGEOMETRY_HEIGHT",
+ screen.height + "");
+ storeLastKnownDimensions("", new Rectangle(getBounds().x, getBounds().y,
+ getWidth(), getHeight()));
if (jconsole != null)
{
if (shortv)
{
message.append("<h1><strong>Version: "
- + jalview.bin.Cache.getProperty("VERSION") + "</strong></h1>");
+ + jalview.bin.Cache.getProperty("VERSION")
+ + "</strong></h1>");
message.append("<strong>Last Updated: <em>"
+ jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
+ "</em></strong>");
+ jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
}
- if (jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking").equals(
- "Checking"))
+ if (jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking")
+ .equals("Checking"))
{
message.append("<br>...Checking latest version...</br>");
}
"..Checking..")
+ " is available for download from "
+ jalview.bin.Cache.getDefault("www.jalview.org",
- "http://www.jalview.org") + " !!");
+ "http://www.jalview.org")
+ + " !!");
if (red)
{
message.append("</div>");
}
}
- message.append("<br>Authors: "
- + jalview.bin.Cache
- .getDefault("AUTHORFNAMES",
- "The Jalview Authors (See AUTHORS file for current list)")
+ message.append("<br>Authors: " + jalview.bin.Cache.getDefault(
+ "AUTHORFNAMES",
+ "The Jalview Authors (See AUTHORS file for current list)")
+ "<br><br>Development managed by The Barton Group, University of Dundee, Scotland, UK.<br>"
+ "<br><br>For help, see the FAQ at <a href=\"http://www.jalview.org/faq\">www.jalview.org/faq</a> and/or join the jalview-discuss@jalview.org mailing list"
+ "<br><br>If you use Jalview, please cite:"
{
showConsole.setSelected(selected);
// TODO: decide if we should update properties file
- Cache.setProperty("SHOW_JAVA_CONSOLE", Boolean.valueOf(selected)
- .toString());
+ Cache.setProperty("SHOW_JAVA_CONSOLE",
+ Boolean.valueOf(selected).toString());
jconsole.setVisible(selected);
}
{
// TODO: refactor to Jalview desktop session controller action.
setProgressBar(MessageManager.formatMessage(
- "label.saving_jalview_project",
- new Object[] { choice.getName() }), choice.hashCode());
+ "label.saving_jalview_project", new Object[]
+ { choice.getName() }), choice.hashCode());
jalview.bin.Cache.setProperty("LAST_DIRECTORY",
choice.getParent());
// TODO catch and handle errors for savestate
new Jalview2XML().saveState(choice);
} catch (OutOfMemoryError oom)
{
- new OOMWarning("Whilst saving current state to "
- + choice.getName(), oom);
+ new OOMWarning(
+ "Whilst saving current state to " + choice.getName(),
+ oom);
} catch (Exception ex)
{
Cache.log.error(
"Problems whilst trying to save to " + choice.getName(),
ex);
- JvOptionPane.showMessageDialog(me, MessageManager.formatMessage(
- "label.error_whilst_saving_current_state_to",
- new Object[] { choice.getName() }), MessageManager
- .getString("label.couldnt_save_project"),
+ JvOptionPane.showMessageDialog(me,
+ MessageManager.formatMessage(
+ "label.error_whilst_saving_current_state_to",
+ new Object[]
+ { choice.getName() }),
+ MessageManager.getString("label.couldnt_save_project"),
JvOptionPane.WARNING_MESSAGE);
}
setProgressBar(null, choice.hashCode());
public void loadState_actionPerformed(ActionEvent e)
{
JalviewFileChooser chooser = new JalviewFileChooser(
- Cache.getProperty("LAST_DIRECTORY"), new String[] {
- "jvp", "jar" }, new String[] { "Jalview Project",
- "Jalview Project (old)" }, "Jalview Project");
+ Cache.getProperty("LAST_DIRECTORY"), new String[]
+ { "jvp", "jar" },
+ new String[]
+ { "Jalview Project", "Jalview Project (old)" },
+ "Jalview Project");
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.restore_state"));
final File selectedFile = chooser.getSelectedFile();
setProjectFile(selectedFile);
final String choice = selectedFile.getAbsolutePath();
- Cache.setProperty("LAST_DIRECTORY",
- selectedFile.getParent());
+ Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
new Thread(new Runnable()
{
@Override
public void run()
{
- setProgressBar(
- MessageManager.formatMessage(
- "label.loading_jalview_project",
- new Object[] { choice }), choice.hashCode());
+ setProgressBar(MessageManager.formatMessage(
+ "label.loading_jalview_project", new Object[]
+ { choice }), choice.hashCode());
try
{
new Jalview2XML().loadJalviewAlign(choice);
new OOMWarning("Whilst loading project from " + choice, oom);
} catch (Exception ex)
{
- Cache.log.error("Problems whilst loading project from "
- + choice, ex);
- JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
- .formatMessage(
+ Cache.log.error(
+ "Problems whilst loading project from " + choice, ex);
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
"label.error_whilst_loading_project_from",
- new Object[] { choice }), MessageManager
- .getString("label.couldnt_load_project"),
+ new Object[]
+ { choice }),
+ MessageManager.getString("label.couldnt_load_project"),
JvOptionPane.WARNING_MESSAGE);
}
setProgressBar(null, choice.hashCode());
{
if (fileLoadingCount == 0)
{
- fileLoadingPanels.add(addProgressPanel(MessageManager.formatMessage(
- "label.loading_file", new Object[] { fileName })));
+ fileLoadingPanels.add(addProgressPanel(MessageManager
+ .formatMessage("label.loading_file", new Object[]
+ { fileName })));
}
fileLoadingCount++;
}
thisprogress.add(progressBar, BorderLayout.CENTER);
progressPanel.add(thisprogress);
- ((GridLayout) progressPanel.getLayout())
- .setRows(((GridLayout) progressPanel.getLayout()).getRows() + 1);
+ ((GridLayout) progressPanel.getLayout()).setRows(
+ ((GridLayout) progressPanel.getLayout()).getRows() + 1);
++totalProgressCount;
instance.validate();
return thisprogress;
for (AlignFrame afr : frames)
{
- if (sequenceSetId == null
- || afr.getViewport().getSequenceSetId()
- .equals(sequenceSetId))
+ if (sequenceSetId == null || afr.getViewport().getSequenceSetId()
+ .equals(sequenceSetId))
{
if (afr.alignPanels != null)
{
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager
- .getString("label.open_saved_vamsas_session"));
- chooser.setToolTipText(MessageManager
- .getString("label.select_vamsas_session_opened_as_new_vamsas_session"));
+ chooser.setDialogTitle(
+ MessageManager.getString("label.open_saved_vamsas_session"));
+ chooser.setToolTipText(MessageManager.getString(
+ "label.select_vamsas_session_opened_as_new_vamsas_session"));
int value = chooser.showOpenDialog(this);
String fle = chooser.getSelectedFile().toString();
if (!vamsasImport(chooser.getSelectedFile()))
{
- JvOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- MessageManager.formatMessage(
- "label.couldnt_import_as_vamsas_session",
- new Object[] { fle }),
- MessageManager
- .getString("label.vamsas_document_import_failed"),
- JvOptionPane.ERROR_MESSAGE);
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.couldnt_import_as_vamsas_session",
+ new Object[]
+ { fle }),
+ MessageManager
+ .getString("label.vamsas_document_import_failed"),
+ JvOptionPane.ERROR_MESSAGE);
}
}
}
else
{
- jalview.bin.Cache.log
- .error("Implementation error - load session from a running session is not supported.");
+ jalview.bin.Cache.log.error(
+ "Implementation error - load session from a running session is not supported.");
}
}
if (v_client != null)
{
- jalview.bin.Cache.log
- .error("Implementation error - load session from a running session is not supported.");
+ jalview.bin.Cache.log.error(
+ "Implementation error - load session from a running session is not supported.");
return false;
}
{
jalview.bin.Cache.log.error(
"Failed to create new vamsas session from contents of URL "
- + url, ex);
+ + url,
+ ex);
return false;
}
setupVamsasConnectedGui();
if (v_client != null)
{
- jalview.bin.Cache.log
- .error("Implementation error - load session from a running session is not supported.");
+ jalview.bin.Cache.log.error(
+ "Implementation error - load session from a running session is not supported.");
return false;
}
setProgressBar(MessageManager.formatMessage(
- "status.importing_vamsas_session_from",
- new Object[] { file.getName() }), file.hashCode());
+ "status.importing_vamsas_session_from", new Object[]
+ { file.getName() }), file.hashCode());
try
{
v_client = new jalview.gui.VamsasApplication(this, file, null);
} catch (Exception ex)
{
setProgressBar(MessageManager.formatMessage(
- "status.importing_vamsas_session_from",
- new Object[] { file.getName() }), file.hashCode());
+ "status.importing_vamsas_session_from", new Object[]
+ { file.getName() }), file.hashCode());
jalview.bin.Cache.log.error(
"New vamsas session from existing session file failed:", ex);
return false;
setupVamsasConnectedGui();
v_client.initial_update(); // TODO: thread ?
setProgressBar(MessageManager.formatMessage(
- "status.importing_vamsas_session_from",
- new Object[] { file.getName() }), file.hashCode());
+ "status.importing_vamsas_session_from", new Object[]
+ { file.getName() }), file.hashCode());
return v_client.inSession();
}
{
if (v_client != null)
{
- throw new Error(
- MessageManager
- .getString("error.try_join_vamsas_session_another"));
+ throw new Error(MessageManager
+ .getString("error.try_join_vamsas_session_another"));
}
if (mysesid == null)
{
vamsasSave.setVisible(false);
vamsasStop.setVisible(false);
vamsasImport.setVisible(true);
- vamsasStart.setText(MessageManager
- .getString("label.new_vamsas_session"));
+ vamsasStart
+ .setText(MessageManager.getString("label.new_vamsas_session"));
}
@Override
sess = VamsasApplication.getSessionList();
} catch (Exception e)
{
- jalview.bin.Cache.log.warn(
- "Problem getting current sessions list.", e);
+ jalview.bin.Cache.log.warn("Problem getting current sessions list.",
+ e);
sess = null;
}
if (sess != null)
{
- jalview.bin.Cache.log.debug("Got current sessions list: "
- + sess.length + " entries.");
+ jalview.bin.Cache.log.debug(
+ "Got current sessions list: " + sess.length + " entries.");
VamsasStMenu.removeAll();
for (int i = 0; i < sess.length; i++)
{
JMenuItem sessit = new JMenuItem();
sessit.setText(sess[i]);
- sessit.setToolTipText(MessageManager.formatMessage(
- "label.connect_to_session", new Object[] { sess[i] }));
+ sessit.setToolTipText(MessageManager
+ .formatMessage("label.connect_to_session", new Object[]
+ { sess[i] }));
final Desktop dsktp = this;
final String mysesid = sess[i];
sessit.addActionListener(new ActionListener()
{
if (v_client != null)
{
- // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
+ // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
JalviewFileChooser chooser = new JalviewFileChooser("vdj",
"Vamsas Document");
if (value == JalviewFileChooser.APPROVE_OPTION)
{
java.io.File choice = chooser.getSelectedFile();
- JPanel progpanel = addProgressPanel(MessageManager.formatMessage(
- "label.saving_vamsas_doc",
- new Object[] { choice.getName() }));
+ JPanel progpanel = addProgressPanel(MessageManager
+ .formatMessage("label.saving_vamsas_doc", new Object[]
+ { choice.getName() }));
Cache.setProperty("LAST_DIRECTORY", choice.getParent());
String warnmsg = null;
String warnttl = null;
{
warnttl = "Serious Problem saving Vamsas Document";
warnmsg = ex.toString();
- jalview.bin.Cache.log.error("Error Whilst saving document to "
- + choice, ex);
+ jalview.bin.Cache.log
+ .error("Error Whilst saving document to " + choice, ex);
} catch (Exception ex)
{
warnttl = "Problem saving Vamsas Document.";
warnmsg = ex.toString();
- jalview.bin.Cache.log.warn("Exception Whilst saving document to "
- + choice, ex);
+ jalview.bin.Cache.log.warn(
+ "Exception Whilst saving document to " + choice, ex);
}
removeProgressPanel(progpanel);
{
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- warnmsg, warnttl, JvOptionPane.ERROR_MESSAGE);
+ warnmsg, warnttl, JvOptionPane.ERROR_MESSAGE);
}
}
}
}
if (b)
{
- vamUpdate = this.addProgressPanel(MessageManager
- .getString("label.updating_vamsas_session"));
+ vamUpdate = this.addProgressPanel(
+ MessageManager.getString("label.updating_vamsas_session"));
}
vamsasStart.setVisible(!b);
vamsasStop.setVisible(!b);
{
check = true;
int barPos = link.indexOf("|");
- String urlMsg = barPos == -1 ? link : link.substring(0,
- barPos) + ": " + link.substring(barPos + 1);
+ String urlMsg = barPos == -1 ? link
+ : link.substring(0, barPos) + ": "
+ + link.substring(barPos + 1);
urls.add(new JLabel(urlMsg));
}
}
JPanel msgPanel = new JPanel();
msgPanel.setLayout(new BoxLayout(msgPanel, BoxLayout.PAGE_AXIS));
msgPanel.add(Box.createVerticalGlue());
- JLabel msg = new JLabel(
- MessageManager
- .getString("label.SEQUENCE_ID_for_DB_ACCESSION1"));
- JLabel msg2 = new JLabel(
- MessageManager
- .getString("label.SEQUENCE_ID_for_DB_ACCESSION2"));
+ JLabel msg = new JLabel(MessageManager
+ .getString("label.SEQUENCE_ID_for_DB_ACCESSION1"));
+ JLabel msg2 = new JLabel(MessageManager
+ .getString("label.SEQUENCE_ID_for_DB_ACCESSION2"));
msgPanel.add(msg);
for (JLabel url : urls)
{
}
}
});
- }
+ }
/**
* Proxy class for JDesktopPane which optionally displays the current memory
FontMetrics fm = g.getFontMetrics();
if (fm != null)
{
- g.drawString(MessageManager.formatMessage(
- "label.memory_stats",
- new Object[] { df.format(totalFreeMemory),
- df.format(maxMemory), df.format(percentUsage) }), 10,
- getHeight() - fm.getHeight());
+ g.drawString(MessageManager.formatMessage("label.memory_stats",
+ new Object[]
+ { df.format(totalFreeMemory), df.format(maxMemory),
+ df.format(percentUsage) }),
+ 10, getHeight() - fm.getHeight());
}
}
}
jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex);
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.getString("label.couldnt_create_groovy_shell"),
+ MessageManager.getString("label.couldnt_create_groovy_shell"),
MessageManager.getString("label.groovy_support_failed"),
JvOptionPane.ERROR_MESSAGE);
}
*/
protected void addQuitHandler()
{
- getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put(
- KeyStroke.getKeyStroke(KeyEvent.VK_Q, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask()), "Quit");
+ getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW)
+ .put(KeyStroke.getKeyStroke(KeyEvent.VK_Q,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()),
+ "Quit");
getRootPane().getActionMap().put("Quit", new AbstractAction()
{
@Override
if (progressBarHandlers == null
|| !progressBars.containsKey(new Long(id)))
{
- throw new Error(
- MessageManager
- .getString("error.call_setprogressbar_before_registering_handler"));
+ throw new Error(MessageManager.getString(
+ "error.call_setprogressbar_before_registering_handler"));
}
progressBarHandlers.put(new Long(id), handler);
final JPanel progressPanel = progressBars.get(new Long(id));
public void actionPerformed(ActionEvent e)
{
handler.cancelActivity(id);
- us.setProgressBar(MessageManager.formatMessage(
- "label.cancelled_params",
- new Object[] { ((JLabel) progressPanel.getComponent(0))
- .getText() }), id);
+ us.setProgressBar(MessageManager
+ .formatMessage("label.cancelled_params", new Object[]
+ { ((JLabel) progressPanel.getComponent(0)).getText() }),
+ id);
}
});
progressPanel.add(cancel, BorderLayout.EAST);
{
if (desktop != null)
{
- AlignmentPanel[] aps = getAlignmentPanels(viewport.getSequenceSetId());
+ AlignmentPanel[] aps = getAlignmentPanels(
+ viewport.getSequenceSetId());
for (int panel = 0; aps != null && panel < aps.length; panel++)
{
if (aps[panel] != null && aps[panel].av == viewport)
if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
- t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer().startDiscoverer(
- changeSupport);
+ t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
+ .startDiscoverer(changeSupport);
}
Thread t3 = null;
{
} catch (Exception e)
{
}
- alive = (t1 != null && t1.isAlive())
- || (t2 != null && t2.isAlive())
+ alive = (t1 != null && t1.isAlive()) || (t2 != null && t2.isAlive())
|| (t3 != null && t3.isAlive())
|| (t0 != null && t0.isAlive());
}
*
* jd.waitForInput();
*/
- JvOptionPane
- .showConfirmDialog(
- Desktop.desktop,
- new JLabel(
- "<html><table width=\"450\"><tr><td>"
- + ermsg
- + "</td></tr></table>"
- + "<p>It may be that you have invalid JABA URLs<br/>in your web service preferences,"
- + "<br>or as a command-line argument, or mis-configured HTTP proxy settings.</p>"
- + "<p>Check the <em>Connections</em> and <em>Web services</em> tab<br/>of the"
- + " Tools->Preferences dialog box to change them.</p></html>"),
- "Web Service Configuration Problem",
- JvOptionPane.DEFAULT_OPTION,
- JvOptionPane.ERROR_MESSAGE);
+ JvOptionPane.showConfirmDialog(Desktop.desktop,
+ new JLabel("<html><table width=\"450\"><tr><td>"
+ + ermsg + "</td></tr></table>"
+ + "<p>It may be that you have invalid JABA URLs<br/>in your web service preferences,"
+ + "<br>or as a command-line argument, or mis-configured HTTP proxy settings.</p>"
+ + "<p>Check the <em>Connections</em> and <em>Web services</em> tab<br/>of the"
+ + " Tools->Preferences dialog box to change them.</p></html>"),
+ "Web Service Configuration Problem",
+ JvOptionPane.DEFAULT_OPTION,
+ JvOptionPane.ERROR_MESSAGE);
serviceChangedDialog = null;
}
}
else
{
- Cache.log
- .error("Errors reported by JABA discovery service. Check web services preferences.\n"
+ Cache.log.error(
+ "Errors reported by JABA discovery service. Check web services preferences.\n"
+ ermsg);
}
}
{
if (progress != null)
{
- progress.setProgressBar(MessageManager.formatMessage(
- "status.opening_params", new Object[] { url }), this
- .hashCode());
+ progress.setProgressBar(MessageManager
+ .formatMessage("status.opening_params", new Object[]
+ { url }), this.hashCode());
}
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception ex)
}
else
{
- System.err.println("Couldn't handle string " + url
- + " as a URL.");
+ System.err.println(
+ "Couldn't handle string " + url + " as a URL.");
}
}
// ignore any exceptions due to dud links.
{
invalidate();
File of;
- ImageMaker im = new jalview.util.ImageMaker(this, ImageMaker.TYPE.EPS,
- "View of Desktop", getWidth(), getHeight(), of = new File(
- "Jalview_snapshot" + System.currentTimeMillis()
- + ".eps"), "View of desktop", null, 0, false);
+ ImageMaker im = new jalview.util.ImageMaker(
+ this, ImageMaker.TYPE.EPS, "View of Desktop", getWidth(),
+ getHeight(), of = new File("Jalview_snapshot"
+ + System.currentTimeMillis() + ".eps"),
+ "View of desktop", null, 0, false);
try
{
paintAll(im.getGraphics());
AlignFrame myBottomFrame = (AlignFrame) source.getBottomFrame();
myTopFrame.viewport.setExplodedGeometry(new Rectangle(source.getX(),
source.getY(), myTopFrame.getWidth(), myTopFrame.getHeight()));
- myBottomFrame.viewport.setExplodedGeometry(new Rectangle(source.getX(),
- source.getY(), myBottomFrame.getWidth(), myBottomFrame
- .getHeight()));
+ myBottomFrame.viewport
+ .setExplodedGeometry(new Rectangle(source.getX(), source.getY(),
+ myBottomFrame.getWidth(), myBottomFrame.getHeight()));
myTopFrame.viewport.setGatherViewsHere(true);
myBottomFrame.viewport.setGatherViewsHere(true);
String topViewId = myTopFrame.viewport.getSequenceSetId();
gatherThis = true;
topPanel.av.setGatherViewsHere(false);
bottomPanel.av.setGatherViewsHere(false);
- topPanel.av.setExplodedGeometry(new Rectangle(sf.getLocation(),
- topFrame.getSize()));
- bottomPanel.av.setExplodedGeometry(new Rectangle(sf
- .getLocation(), bottomFrame.getSize()));
+ topPanel.av.setExplodedGeometry(
+ new Rectangle(sf.getLocation(), topFrame.getSize()));
+ bottomPanel.av.setExplodedGeometry(
+ new Rectangle(sf.getLocation(), bottomFrame.getSize()));
myTopFrame.addAlignmentPanel(topPanel, false);
myBottomFrame.addAlignmentPanel(bottomPanel, false);
}
public static void transferFromDropTarget(List<String> files,
List<DataSourceType> protocols, DropTargetDropEvent evt,
- Transferable t)
- throws Exception
+ Transferable t) throws Exception
{
DataFlavor uriListFlavor = new DataFlavor(
// fallback to text: workaround - on OSX where there's a JVM bug
Cache.log.debug("standard URIListFlavor failed. Trying text");
// try text fallback
- data = (String) t.getTransferData(new DataFlavor(
- "text/plain;class=java.lang.String"));
+ data = (String) t.getTransferData(
+ new DataFlavor("text/plain;class=java.lang.String"));
if (Cache.log.isDebugEnabled())
{
Cache.log.debug("fallback returned " + data);
{
if (data == null || !added)
{
- Cache.log
- .debug("Couldn't resolve drop data. Here are the supported flavors:");
+ Cache.log.debug(
+ "Couldn't resolve drop data. Here are the supported flavors:");
for (DataFlavor fl : t.getTransferDataFlavors())
{
- Cache.log.debug("Supported transfer dataflavor: "
- + fl.toString());
+ Cache.log.debug(
+ "Supported transfer dataflavor: " + fl.toString());
Object df = t.getTransferData(fl);
if (df != null)
{
bg.add(text);
JOptionPane pane = new JOptionPane(null, JvOptionPane.DEFAULT_OPTION,
- JvOptionPane.DEFAULT_OPTION, null, new Object[] { this });
+ JvOptionPane.DEFAULT_OPTION, null, new Object[]
+ { this });
dialog = pane.createDialog(Desktop.desktop, "EPS Rendering options");
dialog.setVisible(true);
this.fr = frender;
this.type = theType;
ap = fr.ap;
- String title = MessageManager.formatMessage(
- "label.graduated_color_for_params", new String[] { theType });
+ String title = MessageManager
+ .formatMessage("label.graduated_color_for_params", new String[]
+ { theType });
initDialogFrame(this, true, blocking, title, 480, 185);
slider.addChangeListener(new ChangeListener()
slider.setEnabled(true);
slider.setValue((int) (cs.getThreshold() * scaleFactor));
thresholdValue.setEnabled(true);
- threshline = new GraphLine((max - min) / 2f, "Threshold", Color.black);
+ threshline = new GraphLine((max - min) / 2f, "Threshold",
+ Color.black);
threshline.value = cs.getThreshold();
}
slider.setEnabled(false);
slider.setOpaque(false);
slider.setPreferredSize(new Dimension(100, 32));
- slider.setToolTipText(MessageManager
- .getString("label.adjust_threshold"));
+ slider.setToolTipText(
+ MessageManager.getString("label.adjust_threshold"));
thresholdValue.setEnabled(false);
thresholdValue.setColumns(7);
jPanel3.setBackground(Color.white);
thresholdIsMin.setBackground(Color.white);
- thresholdIsMin.setText(MessageManager
- .getString("label.threshold_minmax"));
+ thresholdIsMin
+ .setText(MessageManager.getString("label.threshold_minmax"));
thresholdIsMin.setToolTipText(MessageManager
.getString("label.toggle_absolute_relative_display_threshold"));
thresholdIsMin.addActionListener(new ActionListener()
colourByLabel.setBackground(Color.white);
colourByLabel
.setText(MessageManager.getString("label.colour_by_label"));
- colourByLabel
- .setToolTipText(MessageManager
- .getString("label.display_features_same_type_different_label_using_different_colour"));
+ colourByLabel.setToolTipText(MessageManager.getString(
+ "label.display_features_same_type_different_label_using_different_colour"));
colourByLabel.addActionListener(new ActionListener()
{
@Override
/*
* todo not yet implemented: visual indication of feature threshold
*/
- threshline = new GraphLine((max - min) / 2f, "Threshold", Color.black);
+ threshline = new GraphLine((max - min) / 2f, "Threshold",
+ Color.black);
}
if (hasThreshold)
{
if (colourEditor != null)
{
- System.err
- .println("IMPLEMENTATION ISSUE: overwriting action listener for FeatureColourChooser");
+ System.err.println(
+ "IMPLEMENTATION ISSUE: overwriting action listener for FeatureColourChooser");
}
colourEditor = graduatedColorEditor;
}
* @author $author$
* @version $Revision$
*/
-public class FeatureRenderer extends
- jalview.renderer.seqfeatures.FeatureRenderer
+public class FeatureRenderer
+ extends jalview.renderer.seqfeatures.FeatureRenderer
{
/*
* defaults for creating a new feature are the last created
*/
gridPanel = new JPanel(new GridLayout(4, 1));
JPanel choosePanel = new JPanel();
- choosePanel.add(new JLabel(MessageManager
- .getString("label.select_feature")
- + ":"));
+ choosePanel.add(new JLabel(
+ MessageManager.getString("label.select_feature") + ":"));
final JComboBox<String> overlaps = new JComboBox<String>();
for (SequenceFeature sf : features)
{
- String text = sf.getType() + "/" + sf.getBegin() + "-"
- + sf.getEnd() + " (" + sf.getFeatureGroup() + ")";
+ String text = sf.getType() + "/" + sf.getBegin() + "-" + sf.getEnd()
+ + " (" + sf.getFeatureGroup() + ")";
overlaps.addItem(text);
}
choosePanel.add(overlaps);
highlight.addResult(sequences.get(0), sf.getBegin(),
sf.getEnd());
- alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(highlight);
+ alignPanel.getSeqPanel().seqCanvas
+ .highlightSearchResults(highlight);
}
FeatureColourI col = getFeatureStyle(name.getText());
if (col == null)
{
- col = new FeatureColour(ColorUtils
- .createColourFromName(name.getText()));
+ col = new FeatureColour(
+ ColorUtils.createColourFromName(name.getText()));
}
oldcol = fcol = col;
updateColourButton(mainPanel, colour, col);
mainPanel.add(gridPanel, BorderLayout.NORTH);
JPanel descriptionPanel = new JPanel();
- descriptionPanel.add(new JLabel(MessageManager
- .getString("label.description:"),
- JLabel.RIGHT));
+ descriptionPanel.add(new JLabel(
+ MessageManager.getString("label.description:"), JLabel.RIGHT));
description.setFont(JvSwingUtils.getTextAreaFont());
description.setLineWrap(true);
descriptionPanel.add(new JScrollPane(description));
MessageManager.getString("action.cancel") };
}
- String title = create ? MessageManager
- .getString("label.create_new_sequence_features")
+ String title = create
+ ? MessageManager.getString("label.create_new_sequence_features")
: MessageManager.formatMessage("label.amend_delete_features",
- new String[] { sequences.get(0).getName() });
+ new String[]
+ { sequences.get(0).getName() });
/*
* show the dialog
sf.type = enteredType;
sf.featureGroup = group.getText().trim();
sf.description = description.getText().replaceAll("\n", " ");
- boolean refreshSettings = (!featureType.equals(sf.type) || !featureGroup
- .equals(sf.featureGroup));
+ boolean refreshSettings = (!featureType.equals(sf.type)
+ || !featureGroup.equals(sf.featureGroup));
refreshSettings |= (fcol != oldcol);
setColour(sf.type, fcol);
{
String msg = MessageManager.formatMessage("label.warning_hidden",
MessageManager.getString("label.group"), group);
- JvOptionPane.showMessageDialog(panel, msg, "", JvOptionPane.OK_OPTION);
+ JvOptionPane.showMessageDialog(panel, msg, "",
+ JvOptionPane.OK_OPTION);
}
}
import javax.swing.table.TableCellEditor;
import javax.swing.table.TableCellRenderer;
-public class FeatureSettings extends JPanel implements
- FeatureSettingsControllerI
+public class FeatureSettings extends JPanel
+ implements FeatureSettingsControllerI
{
DasSourceBrowser dassourceBrowser;
this.af = af;
fr = af.getFeatureRenderer();
// allow transparency to be recovered
- transparency.setMaximum(100 - (int) ((originalTransparency = fr
- .getTransparency()) * 100));
+ transparency.setMaximum(100
+ - (int) ((originalTransparency = fr.getTransparency()) * 100));
try
{
}
frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
- frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
- {
- @Override
- public void internalFrameClosed(
- javax.swing.event.InternalFrameEvent evt)
- {
- fr.removePropertyChangeListener(change);
- dassourceBrowser.fs = null;
- };
- });
+ frame.addInternalFrameListener(
+ new javax.swing.event.InternalFrameAdapter()
+ {
+ @Override
+ public void internalFrameClosed(
+ javax.swing.event.InternalFrameEvent evt)
+ {
+ fr.removePropertyChangeListener(change);
+ dassourceBrowser.fs = null;
+ };
+ });
frame.setLayer(JLayeredPane.PALETTE_LAYER);
}
{
final FeatureColourI featureColour = (FeatureColourI) typeCol;
- JPopupMenu men = new JPopupMenu(MessageManager.formatMessage(
- "label.settings_for_param", new String[] { type }));
+ JPopupMenu men = new JPopupMenu(MessageManager
+ .formatMessage("label.settings_for_param", new String[]
+ { type }));
JMenuItem scr = new JMenuItem(
MessageManager.getString("label.sort_by_score"));
men.add(scr);
@Override
public void actionPerformed(ActionEvent e)
{
- me.af.avc.sortAlignmentByFeatureScore(Arrays
- .asList(new String[] { type }));
+ me.af.avc
+ .sortAlignmentByFeatureScore(Arrays.asList(new String[]
+ { type }));
}
});
@Override
public void actionPerformed(ActionEvent e)
{
- me.af.avc.sortAlignmentByFeatureDensity(Arrays
- .asList(new String[] { type }));
+ me.af.avc
+ .sortAlignmentByFeatureDensity(Arrays.asList(new String[]
+ { type }));
}
});
else
{
// probably the color chooser!
- table.setValueAt(
- new FeatureColour(colorChooser.getColor()),
+ table.setValueAt(new FeatureColour(colorChooser.getColor()),
selectedRow, 1);
table.validate();
me.updateFeatureRenderer(
false, type);
}
});
- JMenuItem clearCols = new JMenuItem(
- MessageManager.getString("label.select_columns_not_containing"));
+ JMenuItem clearCols = new JMenuItem(MessageManager
+ .getString("label.select_columns_not_containing"));
clearCols.addActionListener(new ActionListener()
{
@Override
data[dataIndex][0] = type;
data[dataIndex][1] = fr.getFeatureStyle(type);
- data[dataIndex][2] = new Boolean(af.getViewport()
- .getFeaturesDisplayed().isVisible(type));
+ data[dataIndex][2] = new Boolean(
+ af.getViewport().getFeaturesDisplayed().isVisible(type));
dataIndex++;
visibleChecks.removeElement(type);
}
table.setModel(new FeatureTableModel(data));
table.getColumnModel().getColumn(0).setPreferredWidth(200);
- groupPanel.setLayout(new GridLayout(fr.getFeatureGroupsSize() / 4 + 1,
- 4));
+ groupPanel.setLayout(
+ new GridLayout(fr.getFeatureGroupsSize() / 4 + 1, 4));
pruneGroups(foundGroups);
groupPanel.validate();
JalviewFileChooser chooser = new JalviewFileChooser("fc",
"Sequence Feature Colours");
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager
- .getString("label.load_feature_colours"));
+ chooser.setDialogTitle(
+ MessageManager.getString("label.load_feature_colours"));
chooser.setToolTipText(MessageManager.getString("action.load"));
int value = chooser.showOpenDialog(this);
try
{
- InputStreamReader in = new InputStreamReader(new FileInputStream(
- file), "UTF-8");
+ InputStreamReader in = new InputStreamReader(
+ new FileInputStream(file), "UTF-8");
JalviewUserColours jucs = JalviewUserColours.unmarshal(in);
JalviewFileChooser chooser = new JalviewFileChooser("fc",
"Sequence Feature Colours");
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager
- .getString("label.save_feature_colours"));
+ chooser.setDialogTitle(
+ MessageManager.getString("label.save_feature_colours"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
col.setRGB(Format.getHexString(fcol.getMaxColour()));
col.setMin(fcol.getMin());
col.setMax(fcol.getMax());
- col.setMinRGB(jalview.util.Format.getHexString(fcol
- .getMinColour()));
+ col.setMinRGB(
+ jalview.util.Format.getHexString(fcol.getMinColour()));
col.setAutoScale(fcol.isAutoScaled());
col.setThreshold(fcol.getThreshold());
col.setColourByLabel(fcol.isColourByLabel());
- col.setThreshType(fcol.isAboveThreshold() ? "ABOVE" : (fcol
- .isBelowThreshold() ? "BELOW" : "NONE"));
+ col.setThreshType(fcol.isAboveThreshold() ? "ABOVE"
+ : (fcol.isBelowThreshold() ? "BELOW" : "NONE"));
}
ucs.addColour(col);
}
}
});
sortByDens.setFont(JvSwingUtils.getLabelFont());
- sortByDens.setText(MessageManager
- .getString("label.sequence_sort_by_density"));
+ sortByDens.setText(
+ MessageManager.getString("label.sequence_sort_by_density"));
sortByDens.addActionListener(new ActionListener()
{
@Override
});
transparency.setMaximum(70);
- transparency.setToolTipText(MessageManager
- .getString("label.transparency_tip"));
+ transparency.setToolTipText(
+ MessageManager.getString("label.transparency_tip"));
fetchDAS.setText(MessageManager.getString("label.fetch_das_features"));
fetchDAS.addActionListener(new ActionListener()
{
public void noDasSourceActive()
{
complete();
- JvOptionPane
- .showInternalConfirmDialog(
- Desktop.desktop,
- MessageManager
- .getString("label.no_das_sources_selected_warn"),
- MessageManager
- .getString("label.no_das_sources_selected_title"),
- JvOptionPane.DEFAULT_OPTION,
- JvOptionPane.INFORMATION_MESSAGE);
+ JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ MessageManager.getString("label.no_das_sources_selected_warn"),
+ MessageManager.getString("label.no_das_sources_selected_title"),
+ JvOptionPane.DEFAULT_OPTION, JvOptionPane.INFORMATION_MESSAGE);
}
// ///////////////////////////////////////////////////////////////////////
}
@Override
- public Component getTableCellRendererComponent(JTable tbl,
- Object color, boolean isSelected, boolean hasFocus, int row,
- int column)
+ public Component getTableCellRendererComponent(JTable tbl, Object color,
+ boolean isSelected, boolean hasFocus, int row, int column)
{
FeatureColourI cellColour = (FeatureColourI) color;
// JLabel comp = new JLabel();
}
}
-class ColorEditor extends AbstractCellEditor implements TableCellEditor,
- ActionListener
+class ColorEditor extends AbstractCellEditor
+ implements TableCellEditor, ActionListener
{
FeatureSettings me;
frame = new JInternalFrame();
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
- frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
- {
- @Override
- public void internalFrameClosing(InternalFrameEvent e)
- {
- closeAction();
- }
- });
+ frame.addInternalFrameListener(
+ new javax.swing.event.InternalFrameAdapter()
+ {
+ @Override
+ public void internalFrameClosing(InternalFrameEvent e)
+ {
+ closeAction();
+ }
+ });
addEscapeHandler();
Desktop.addInternalFrame(frame, MessageManager.getString("label.find"),
MY_WIDTH, MY_HEIGHT);
*/
private void addEscapeHandler()
{
- getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put(
- KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0), "Cancel");
+ getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW)
+ .put(KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0), "Cancel");
getRootPane().getActionMap().put("Cancel", new AbstractAction()
{
@Override
});
}
-
/**
* Performs the 'Find Next' action.
*
for (SearchResultMatchI match : searchResults.getResults())
{
seqs.add(match.getSequence().getDatasetSequence());
- features.add(new SequenceFeature(searchString, desc, null, match
- .getStart(), match.getEnd(), desc));
+ features.add(new SequenceFeature(searchString, desc, null,
+ match.getStart(), match.getEnd(), desc));
}
if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
if (doFindAll)
{
// then we report the matches that were found
- String message = (idMatch.size() > 0) ? "" + idMatch.size()
- + " IDs" : "";
+ String message = (idMatch.size() > 0) ? "" + idMatch.size() + " IDs"
+ : "";
if (searchResults != null)
{
if (idMatch.size() > 0 && searchResults.getSize() > 0)
{
oldComplementFont = ((AlignViewport) ap.av.getCodingComplement())
.getFont();
- oldComplementSmooth = ((AlignViewport) ap.av.getCodingComplement()).antiAlias;
+ oldComplementSmooth = ((AlignViewport) ap.av
+ .getCodingComplement()).antiAlias;
scaleAsCdna.setVisible(true);
scaleAsCdna.setSelected(ap.av.isScaleProteinAsCdna());
fontAsCdna.setVisible(true);
fontStyle.setSelectedIndex(oldFont.getStyle());
FontMetrics fm = getGraphics().getFontMetrics(oldFont);
- monospaced.setSelected(fm.getStringBounds("M", getGraphics())
- .getWidth() == fm.getStringBounds("|", getGraphics())
- .getWidth());
+ monospaced.setSelected(
+ fm.getStringBounds("M", getGraphics()).getWidth() == fm
+ .getStringBounds("|", getGraphics()).getWidth());
init = false;
}
ap.paintAlignment(true);
if (ap.av.getCodingComplement() != null && ap.av.isProteinFontAsCdna())
{
- ((AlignViewport) ap.av.getCodingComplement()).antiAlias = ap.av.antiAlias;
+ ((AlignViewport) ap.av
+ .getCodingComplement()).antiAlias = ap.av.antiAlias;
SplitFrame sv = (SplitFrame) ap.alignFrame.getSplitViewContainer();
sv.adjustLayout();
sv.repaint();
{
ap.av.getCodingComplement().setScaleProteinAsCdna(oldProteinScale);
ap.av.getCodingComplement().setProteinFontAsCdna(oldMirrorFont);
- ((AlignViewport) ap.av.getCodingComplement()).antiAlias = oldComplementSmooth;
+ ((AlignViewport) ap.av
+ .getCodingComplement()).antiAlias = oldComplementSmooth;
ap.av.getCodingComplement().setFont(oldComplementFont, true);
SplitFrame splitFrame = (SplitFrame) ap.alignFrame
.getSplitViewContainer();
double iw = iBounds.getWidth();
if (mw < 1 || iw < 1)
{
- String message = iBounds.getHeight() < 1 ? MessageManager
- .getString("label.font_doesnt_have_letters_defined")
+ String message = iBounds.getHeight() < 1
+ ? MessageManager
+ .getString("label.font_doesnt_have_letters_defined")
: MessageManager.getString("label.font_too_small");
JvOptionPane.showInternalMessageDialog(this, message,
MessageManager.getString("label.invalid_font"),
{
fontSize.setSelectedItem(lastSelected.getSize());
}
- if (!lastSelected.getName().equals(
- fontName.getSelectedItem().toString()))
+ if (!lastSelected.getName()
+ .equals(fontName.getSelectedItem().toString()))
{
fontName.setSelectedItem(lastSelected.getName());
}
protected void scaleAsCdna_actionPerformed()
{
ap.av.setScaleProteinAsCdna(scaleAsCdna.isSelected());
- ap.av.getCodingComplement().setScaleProteinAsCdna(
- scaleAsCdna.isSelected());
+ ap.av.getCodingComplement()
+ .setScaleProteinAsCdna(scaleAsCdna.isSelected());
final SplitFrame splitFrame = (SplitFrame) ap.alignFrame
.getSplitViewContainer();
splitFrame.adjustLayout();
bg.add(text);
JOptionPane pane = new JOptionPane(null, JvOptionPane.DEFAULT_OPTION,
- JvOptionPane.DEFAULT_OPTION, null, new Object[] { this });
+ JvOptionPane.DEFAULT_OPTION, null, new Object[]
+ { this });
dialog = pane.createDialog(Desktop.desktop, "HTML Rendering options");
dialog.setVisible(true);
{
if (av.isSeqNameItalics())
{
- setIdfont(new Font(av.getFont().getName(), Font.ITALIC, av.getFont()
- .getSize()));
+ setIdfont(new Font(av.getFont().getName(), Font.ITALIC,
+ av.getFont().getSize()));
}
else
{
currentColor = Color.black;
currentTextColor = Color.white;
}
- else if ((av.getSelectionGroup() != null)
- && av.getSelectionGroup().getSequences(null)
- .contains(sequence))
+ else if ((av.getSelectionGroup() != null) && av.getSelectionGroup()
+ .getSequences(null).contains(sequence))
{
currentColor = Color.lightGray;
currentTextColor = Color.black;
void drawMarker(int i, int starty, int yoffset)
{
- SequenceI[] hseqs = av.getAlignment().getHiddenSequences().hiddenSequences;
+ SequenceI[] hseqs = av.getAlignment()
+ .getHiddenSequences().hiddenSequences;
// Use this method here instead of calling hiddenSeq adjust
// 3 times.
int hSize = hseqs.length;
if (below)
{
gg.fillPolygon(
- new int[] { getWidth() - av.getCharHeight(),
+ new int[]
+ { getWidth() - av.getCharHeight(),
getWidth() - av.getCharHeight(), getWidth() },
- new int[] {
- (i - starty) * av.getCharHeight() + yoffset,
+ new int[]
+ { (i - starty) * av.getCharHeight() + yoffset,
(i - starty) * av.getCharHeight() + yoffset
+ av.getCharHeight() / 4,
- (i - starty) * av.getCharHeight() + yoffset }, 3);
+ (i - starty) * av.getCharHeight() + yoffset },
+ 3);
}
if (above)
{
gg.fillPolygon(
- new int[] { getWidth() - av.getCharHeight(),
+ new int[]
+ { getWidth() - av.getCharHeight(),
getWidth() - av.getCharHeight(), getWidth() },
- new int[] {
- (i - starty + 1) * av.getCharHeight() + yoffset,
+ new int[]
+ { (i - starty + 1) * av.getCharHeight() + yoffset,
(i - starty + 1) * av.getCharHeight() + yoffset
- av.getCharHeight() / 4,
- (i - starty + 1) * av.getCharHeight() + yoffset }, 3);
+ (i - starty + 1) * av.getCharHeight() + yoffset },
+ 3);
}
}
void setHiddenFont(SequenceI seq)
{
- Font bold = new Font(av.getFont().getName(), Font.BOLD, av.getFont()
- .getSize());
+ Font bold = new Font(av.getFont().getName(), Font.BOLD,
+ av.getFont().getSize());
if (av.isReferenceSeq(seq) || av.isHiddenRepSequence(seq))
{
{
String propertyName = evt.getPropertyName();
if (propertyName.equals(ViewportRanges.STARTSEQ)
- || (av.getWrapAlignment() && propertyName
- .equals(ViewportRanges.STARTRES)))
+ || (av.getWrapAlignment()
+ && propertyName.equals(ViewportRanges.STARTRES)))
{
fastPaint((int) evt.getNewValue() - (int) evt.getOldValue());
}
* @author $author$
* @version $Revision$
*/
-public class IdPanel extends JPanel implements MouseListener,
- MouseMotionListener, MouseWheelListener
+public class IdPanel extends JPanel
+ implements MouseListener, MouseMotionListener, MouseWheelListener
{
private IdCanvas idCanvas;
}
if ((av.getSelectionGroup() == null)
- || (!jalview.util.Platform.isControlDown(e) && !e.isShiftDown() && av
- .getSelectionGroup() != null))
+ || (!jalview.util.Platform.isControlDown(e) && !e.isShiftDown()
+ && av.getSelectionGroup() != null))
{
av.setSelectionGroup(new SequenceGroup());
av.getSelectionGroup().setStartRes(0);
for (int i = start; i <= end; i++)
{
- av.getSelectionGroup().addSequence(
- av.getAlignment().getSequenceAt(i), i == end);
+ av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
+ i == end);
}
}
* @author $author$
* @version $Revision$
*/
-public class IdwidthAdjuster extends JPanel implements MouseListener,
- MouseMotionListener
+public class IdwidthAdjuster extends JPanel
+ implements MouseListener, MouseMotionListener
{
boolean active = false;
public JDatabaseTree(jalview.ws.SequenceFetcher sfetch)
{
mainPanel.add(this);
- initDialogFrame(mainPanel, true, false,
- MessageManager
- .getString("label.select_database_retrieval_source"),
- 650, 490);
+ initDialogFrame(mainPanel, true, false, MessageManager
+ .getString("label.select_database_retrieval_source"), 650, 490);
/*
* Dynamically generated database list will need a translation function from
* internal source to externally distinct names. UNIPROT and UP_NAME are
dbviews = new JTree(new DefaultTreeModel(root, false));
dbviews.setCellRenderer(new DbTreeRenderer(this));
- dbviews.getSelectionModel().setSelectionMode(
- TreeSelectionModel.SINGLE_TREE_SELECTION);
+ dbviews.getSelectionModel()
+ .setSelectionMode(TreeSelectionModel.SINGLE_TREE_SELECTION);
svp = new JScrollPane(dbviews);
svp.setMinimumSize(new Dimension(100, 200));
svp.setPreferredSize(new Dimension(200, 400));
}
}
});
- JPanel jc = new JPanel(new BorderLayout()), j = new JPanel(
- new FlowLayout());
+ JPanel jc = new JPanel(new BorderLayout()),
+ j = new JPanel(new FlowLayout());
jc.add(svp, BorderLayout.CENTER);
java.awt.Font f;
}
else
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_cant_reorder_tree"));
+ throw new Error(MessageManager
+ .getString("error.implementation_error_cant_reorder_tree"));
}
}
jalview.util.QuickSort.sort(names, nodes);
}
}
- private class DbTreeRenderer extends DefaultTreeCellRenderer implements
- TreeCellRenderer
+ private class DbTreeRenderer extends DefaultTreeCellRenderer
+ implements TreeCellRenderer
{
JDatabaseTree us;
{
for (TreePath tp : tsel)
{
- DefaultMutableTreeNode admt, dmt = (DefaultMutableTreeNode) tp
- .getLastPathComponent();
+ DefaultMutableTreeNode admt,
+ dmt = (DefaultMutableTreeNode) tp.getLastPathComponent();
if (dmt.getUserObject() != null)
{
/*
{
if (allowMultiSelections)
{
- srcs.addAll(sfetcher.getSourceProxy((String) dmt
- .getUserObject()));
+ srcs.addAll(sfetcher
+ .getSourceProxy((String) dmt.getUserObject()));
}
else
{
- srcs.add(sfetcher
- .getSourceProxy((String) dmt.getUserObject()).get(0));
+ srcs.add(sfetcher.getSourceProxy((String) dmt.getUserObject())
+ .get(0));
forcedFirstChild = true;
}
}
if (allowMultiSelections)
{
dbstatus.setText(MessageManager.formatMessage(
- "label.selected_database_to_fetch_from", new String[] {
- Integer.valueOf(srcs.size()).toString(),
+ "label.selected_database_to_fetch_from", new String[]
+ { Integer.valueOf(srcs.size()).toString(),
(srcs.size() == 1 ? "" : "s"),
- (srcs.size() > 0 ? " with " + x + " test quer"
- + (x == 1 ? "y" : "ies") : ".") }));
+ (srcs.size() > 0
+ ? " with " + x + " test quer"
+ + (x == 1 ? "y" : "ies")
+ : ".") }));
}
else
{
if (nm.length() > 0)
{
- dbstatus.setText(MessageManager.formatMessage(
- "label.database_param", new String[] { nm }));
+ dbstatus.setText(MessageManager
+ .formatMessage("label.database_param", new String[]
+ { nm }));
if (qr.length() > 0)
{
- dbstatex.setText(MessageManager.formatMessage(
- "label.example_param", new String[] { qr }));
+ dbstatex.setText(MessageManager
+ .formatMessage("label.example_param", new String[]
+ { qr }));
}
}
else
}
public SeqFref newAlcodMapRef(final String sref,
- final AlignedCodonFrame _cf, final jalview.datamodel.Mapping _jmap)
+ final AlignedCodonFrame _cf,
+ final jalview.datamodel.Mapping _jmap)
{
SeqFref fref = new SeqFref(sref, "Codon Frame")
}
} catch (Exception x)
{
- System.err
- .println("IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence "
+ System.err.println(
+ "IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence "
+ ref.getSref());
x.printStackTrace();
failedtoresolve++;
}
if (incompleteSeqs != null && incompleteSeqs.size() > 0)
{
- System.err.println("Jalview Project Import: There are "
- + incompleteSeqs.size()
- + " sequences which may have incomplete metadata.");
+ System.err.println(
+ "Jalview Project Import: There are " + incompleteSeqs.size()
+ + " sequences which may have incomplete metadata.");
if (incompleteSeqs.size() < 10)
{
for (SequenceI s : incompleteSeqs.values())
}
else
{
- System.err
- .println("Too many to report. Skipping output of incomplete sequences.");
+ System.err.println(
+ "Too many to report. Skipping output of incomplete sequences.");
}
}
}
{
AlignFrame af = frames.get(i);
// skip ?
- if (skipList != null
- && skipList
- .containsKey(af.getViewport().getSequenceSetId()))
+ if (skipList != null && skipList
+ .containsKey(af.getViewport().getSequenceSetId()))
{
continue;
}
saveState(apanel, fileName, jout, viewIds);
- String dssid = getDatasetIdRef(af.getViewport().getAlignment()
- .getDataset());
+ String dssid = getDatasetIdRef(
+ af.getViewport().getAlignment().getDataset());
if (!dsses.containsKey(dssid))
{
dsses.put(dssid, af);
if (shortName.indexOf(File.separatorChar) > -1)
{
- shortName = shortName.substring(shortName
- .lastIndexOf(File.separatorChar) + 1);
+ shortName = shortName
+ .substring(shortName.lastIndexOf(File.separatorChar) + 1);
}
int count = 1;
object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
- object.setVersion(jalview.bin.Cache.getDefault("VERSION",
- "Development Build"));
+ object.setVersion(
+ jalview.bin.Cache.getDefault("VERSION", "Development Build"));
/**
* rjal is full height alignment, jal is actual alignment with full metadata
if (av.hasHiddenRows())
{
// use rjal, contains the full height alignment
- jseq.setHidden(av.getAlignment().getHiddenSequences()
- .isHidden(jds));
+ jseq.setHidden(
+ av.getAlignment().getHiddenSequences().isHidden(jds));
if (av.isHiddenRepSequence(jds))
{
if (frames[f] instanceof StructureViewerBase)
{
StructureViewerBase viewFrame = (StructureViewerBase) frames[f];
- matchedFile = saveStructureState(ap, jds, pdb, entry,
- viewIds, matchedFile, viewFrame);
+ matchedFile = saveStructureState(ap, jds, pdb, entry, viewIds,
+ matchedFile, viewFrame);
/*
* Only store each structure viewer's state once in the project
* jar. First time through only (storeDS==false)
viewerState.getBytes());
} catch (IOException e)
{
- System.err.println("Error saving viewer state: "
- + e.getMessage());
+ System.err.println(
+ "Error saving viewer state: " + e.getMessage());
}
}
}
{
AlcodMap alcmap = new AlcodMap();
alcmap.setDnasq(seqHash(dnas[m]));
- alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
- false));
+ alcmap.setMapping(
+ createVamsasMapping(pmaps[m], dnas[m], null, false));
alc.addAlcodMap(alcmap);
hasMap = true;
}
ColourSchemeI colourScheme = sg.getColourScheme();
if (colourScheme != null)
{
- ResidueShaderI groupColourScheme = sg
- .getGroupColourScheme();
+ ResidueShaderI groupColourScheme = sg.getGroupColourScheme();
if (groupColourScheme.conservationApplied())
{
jGroup.setConsThreshold(groupColourScheme.getConservationInc());
if (colourScheme instanceof jalview.schemes.UserColourScheme)
{
- jGroup.setColour(setUserColourScheme(colourScheme,
- userColours, jms));
+ jGroup.setColour(
+ setUserColourScheme(colourScheme, userColours, jms));
}
else
{
}
else if (colourScheme instanceof jalview.schemes.UserColourScheme)
{
- jGroup.setColour(setUserColourScheme(colourScheme,
- userColours, jms));
+ jGroup.setColour(
+ setUserColourScheme(colourScheme, userColours, jms));
}
else
{
// /////////SAVE VIEWPORT
Viewport view = new Viewport();
view.setTitle(ap.alignFrame.getTitle());
- view.setSequenceSetId(makeHashCode(av.getSequenceSetId(),
- av.getSequenceSetId()));
+ view.setSequenceSetId(
+ makeHashCode(av.getSequenceSetId(), av.getSequenceSetId()));
view.setId(av.getViewId());
if (av.getCodingComplement() != null)
{
view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(),
userColours, jms));
}
- else if (av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
+ else if (av
+ .getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
{
AnnotationColours ac = constructAnnotationColours(
(jalview.schemes.AnnotationColourGradient) av
}
else
{
- view.setBgColour(ColourSchemeProperty.getColourName(av
- .getGlobalColourScheme()));
+ view.setBgColour(ColourSchemeProperty
+ .getColourName(av.getGlobalColourScheme()));
}
ResidueShaderI vcs = av.getResidueShading();
setting.setAutoScale(fcol.isAutoScaled());
setting.setThreshold(fcol.getThreshold());
// -1 = No threshold, 0 = Below, 1 = Above
- setting.setThreshstate(fcol.isAboveThreshold() ? 1 : (fcol
- .isBelowThreshold() ? 0 : -1));
+ setting.setThreshstate(fcol.isAboveThreshold() ? 1
+ : (fcol.isBelowThreshold() ? 0 : -1));
}
else
{
setting.setColour(fcol.getColour().getRGB());
}
- setting.setDisplay(av.getFeaturesDisplayed().isVisible(
- featureType));
+ setting.setDisplay(
+ av.getFeaturesDisplayed().isVisible(featureType));
float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
.getOrder(featureType);
if (rorder > -1)
g.setName(grp);
g.setDisplay(((Boolean) ap.getSeqPanel().seqCanvas
.getFeatureRenderer().checkGroupVisibility(grp, false))
- .booleanValue());
+ .booleanValue());
fs.addGroup(g);
groupsAdded.addElement(grp);
}
}
else
{
- ArrayList<int[]> hiddenRegions = hidden
- .getHiddenColumnsCopy();
+ ArrayList<int[]> hiddenRegions = hidden.getHiddenColumnsCopy();
for (int[] region : hiddenRegions)
{
HiddenColumns hc = new HiddenColumns();
System.out.println("Writing jar entry " + fileName);
JarEntry entry = new JarEntry(fileName);
jout.putNextEntry(entry);
- PrintWriter pout = new PrintWriter(new OutputStreamWriter(jout,
- UTF_8));
+ PrintWriter pout = new PrintWriter(
+ new OutputStreamWriter(jout, UTF_8));
Marshaller marshaller = new Marshaller(pout);
marshaller.marshal(object);
pout.flush();
final PDBEntry pdbentry = bindingModel.getPdbEntry(peid);
final String pdbId = pdbentry.getId();
if (!pdbId.equals(entry.getId())
- && !(entry.getId().length() > 4 && entry.getId()
- .toLowerCase().startsWith(pdbId.toLowerCase())))
+ && !(entry.getId().length() > 4 && entry.getId().toLowerCase()
+ .startsWith(pdbId.toLowerCase())))
{
/*
* not interested in a binding to a different PDB entry here
}
else if (!matchedFile.equals(pdbentry.getFile()))
{
- Cache.log
- .warn("Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
+ Cache.log.warn(
+ "Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
+ pdbentry.getFile());
}
// record the
// match is ambiguous (e.g.
// 1QIP==1qipA)
- for (int smap = 0; smap < viewFrame.getBinding().getSequence()[peid].length; smap++)
+ for (int smap = 0; smap < viewFrame.getBinding()
+ .getSequence()[peid].length; smap++)
{
// if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
if (jds == viewFrame.getBinding().getSequence()[peid][smap])
ac.setAnnotation(acg.getAnnotation().annotationId);
if (acg.getBaseColour() instanceof UserColourScheme)
{
- ac.setColourScheme(setUserColourScheme(acg.getBaseColour(),
- userColours, jms));
+ ac.setColourScheme(
+ setUserColourScheme(acg.getBaseColour(), userColours, jms));
}
else
{
- ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));
+ ac.setColourScheme(
+ ColourSchemeProperty.getColourName(acg.getBaseColour()));
}
ac.setMaxColour(acg.getMaxColour().getRGB());
if (groupIdr == null)
{
// make a locally unique String
- groupRefs.put(
- annotation.groupRef,
+ groupRefs.put(annotation.groupRef,
groupIdr = ("" + System.currentTimeMillis()
- + annotation.groupRef.getName() + groupRefs
- .size()));
+ + annotation.groupRef.getName()
+ + groupRefs.size()));
}
an.setGroupRef(groupIdr.toString());
}
}
if (annotation.annotations[a].displayCharacter != null)
{
- ae.setDisplayCharacter(annotation.annotations[a].displayCharacter);
+ ae.setDisplayCharacter(
+ annotation.annotations[a].displayCharacter);
}
if (!Float.isNaN(annotation.annotations[a].value))
ae.setPosition(a);
if (annotation.annotations[a].secondaryStructure > ' ')
{
- ae.setSecondaryStructure(annotation.annotations[a].secondaryStructure
- + "");
+ ae.setSecondaryStructure(
+ annotation.annotations[a].secondaryStructure + "");
}
if (annotation.annotations[a].colour != null
// need to be able to recover 1) settings 2) user-defined presets or
// recreate settings from preset 3) predefined settings provided by
// service - or settings that can be transferred (or discarded)
- vCalcIdParam.setParameters(settings.getWsParamFile().replace("\n",
- "|\\n|"));
+ vCalcIdParam.setParameters(
+ settings.getWsParamFile().replace("\n", "|\\n|"));
vCalcIdParam.setAutoUpdate(settings.isAutoUpdate());
// todo - decide if updateImmediately is needed for any projects.
}
}
throw new Error(MessageManager.formatMessage(
- "error.unsupported_version_calcIdparam",
- new Object[] { calcIdParam.toString() }));
+ "error.unsupported_version_calcIdparam", new Object[]
+ { calcIdParam.toString() }));
}
/**
for (int i = 0; i < 24; i++)
{
- newColours[i] = new java.awt.Color(Integer.parseInt(colours
- .getUserColourScheme().getColour(i).getRGB(), 16));
+ newColours[i] = new java.awt.Color(Integer.parseInt(
+ colours.getUserColourScheme().getColour(i).getRGB(), 16));
}
jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
newColours = new java.awt.Color[23];
for (int i = 0; i < 23; i++)
{
- newColours[i] = new java.awt.Color(Integer.parseInt(colours
- .getUserColourScheme().getColour(i + 24).getRGB(), 16));
+ newColours[i] = new java.awt.Color(Integer.parseInt(
+ colours.getUserColourScheme().getColour(i + 24).getRGB(),
+ 16));
}
ucs.setLowerCaseColours(newColours);
}
if (true) // !skipViewport(object))
{
_af = loadFromObject(object, file, true, jprovider);
- if (_af != null
- && object.getJalviewModelSequence().getViewportCount() > 0)
+ if (_af != null && object.getJalviewModelSequence()
+ .getViewportCount() > 0)
{
if (af == null)
{
{
ex.printStackTrace();
errorMessage = "Couldn't locate Jalview XML file : " + file;
- System.err.println("Exception whilst loading jalview XML file : "
- + ex + "\n");
+ System.err.println(
+ "Exception whilst loading jalview XML file : " + ex + "\n");
} catch (Exception ex)
{
System.err.println("Parsing as Jalview Version 2 file failed.");
}
ex.printStackTrace();
- System.err.println("Exception whilst loading jalview XML file : "
- + ex + "\n");
+ System.err.println(
+ "Exception whilst loading jalview XML file : " + ex + "\n");
} catch (OutOfMemoryError e)
{
// Don't use the OOM Window here
{
if (ds.getCodonFrames() != null)
{
- StructureSelectionManager.getStructureSelectionManager(
- Desktop.instance).registerMappings(ds.getCodonFrames());
+ StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance)
+ .registerMappings(ds.getCodonFrames());
}
}
if (errorMessage != null)
@Override
public void run()
{
- JvOptionPane
- .showInternalMessageDialog(Desktop.desktop,
- finalErrorMessage, "Error "
- + (saving ? "saving" : "loading")
- + " Jalview file",
- JvOptionPane.WARNING_MESSAGE);
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ finalErrorMessage,
+ "Error " + (saving ? "saving" : "loading")
+ + " Jalview file",
+ JvOptionPane.WARNING_MESSAGE);
}
});
}
if (tmpSeq.getStart() != jseqs[i].getStart()
|| tmpSeq.getEnd() != jseqs[i].getEnd())
{
- System.err
- .println("Warning JAL-2154 regression: updating start/end for sequence "
+ System.err.println(
+ "Warning JAL-2154 regression: updating start/end for sequence "
+ tmpSeq.toString() + " to " + jseqs[i]);
}
}
}
else
{
- boolean isdsal = object.getJalviewModelSequence().getViewportCount() == 0;
+ boolean isdsal = object.getJalviewModelSequence()
+ .getViewportCount() == 0;
if (isdsal)
{
// we are importing a dataset record, so
{
// adds dbrefs to datasequence's set (since Jalview 2.10)
addDBRefs(
- al.getSequenceAt(i).getDatasetSequence() == null ? al.getSequenceAt(i)
+ al.getSequenceAt(i).getDatasetSequence() == null
+ ? al.getSequenceAt(i)
: al.getSequenceAt(i).getDatasetSequence(),
vamsasSeq[i]);
}
}
}
}
- StructureSelectionManager.getStructureSelectionManager(
- Desktop.instance).registerPDBEntry(entry);
+ StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance)
+ .registerPDBEntry(entry);
// adds PDBEntry to datasequence's set (since Jalview 2.10)
if (al.getSequenceAt(i).getDatasetSequence() != null)
{
else
{
// defer to later
- frefedSequence.add(newAlcodMapRef(maps[m].getDnasq(), cf,
- mapping));
+ frefedSequence.add(
+ newAlcodMapRef(maps[m].getDnasq(), cf, mapping));
}
}
}
annotation.setAutoCalculated(true);
}
}
- if (autoForView
- || (annotation.hasAutoCalculated() && annotation
- .isAutoCalculated()))
+ if (autoForView || (annotation.hasAutoCalculated()
+ && annotation.isAutoCalculated()))
{
// remove ID - we don't recover annotation from other views for
// view-specific annotation
anot[anpos] = new jalview.datamodel.Annotation(
- ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
- (ae[aa].getSecondaryStructure() == null || ae[aa]
- .getSecondaryStructure().length() == 0) ? ' '
- : ae[aa].getSecondaryStructure().charAt(0),
+ ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
+ (ae[aa].getSecondaryStructure() == null
+ || ae[aa].getSecondaryStructure().length() == 0)
+ ? ' '
+ : ae[aa].getSecondaryStructure()
+ .charAt(0),
ae[aa].getValue()
);
jaa._linecolour = firstColour;
if (annotation.getThresholdLine() != null)
{
- jaa.setThreshold(new jalview.datamodel.GraphLine(annotation
- .getThresholdLine().getValue(), annotation
- .getThresholdLine().getLabel(), new java.awt.Color(
- annotation.getThresholdLine().getColour())));
+ jaa.setThreshold(new jalview.datamodel.GraphLine(
+ annotation.getThresholdLine().getValue(),
+ annotation.getThresholdLine().getLabel(),
+ new java.awt.Color(
+ annotation.getThresholdLine().getColour())));
}
if (autoForView || annotation.isAutoCalculated())
}
else
{
- cs = ColourSchemeProperty.getColourScheme(al, jGroup.getColour());
+ cs = ColourSchemeProperty.getColourScheme(al,
+ jGroup.getColour());
}
}
int pidThreshold = jGroup.getPidThreshold();
jGroup.getDisplayBoxes(), jGroup.getDisplayText(),
jGroup.getColourText(), jGroup.getStart(), jGroup.getEnd());
sg.getGroupColourScheme().setThreshold(pidThreshold, true);
- sg.getGroupColourScheme().setConservationInc(jGroup.getConsThreshold());
+ sg.getGroupColourScheme()
+ .setConservationInc(jGroup.getConsThreshold());
sg.setOutlineColour(new java.awt.Color(jGroup.getOutlineColour()));
sg.textColour = new java.awt.Color(jGroup.getTextCol1());
sg.textColour2 = new java.awt.Color(jGroup.getTextCol2());
- sg.setShowNonconserved(jGroup.hasShowUnconserved() ? jGroup
- .isShowUnconserved() : false);
+ sg.setShowNonconserved(
+ jGroup.hasShowUnconserved() ? jGroup.isShowUnconserved()
+ : false);
sg.thresholdTextColour = jGroup.getTextColThreshold();
if (jGroup.hasShowConsensusHistogram())
{
}
if (jGroup.getConsThreshold() != 0)
{
- Conservation c = new Conservation("All", sg.getSequences(null),
- 0, sg.getWidth() - 1);
+ Conservation c = new Conservation("All", sg.getSequences(null), 0,
+ sg.getWidth() - 1);
c.calculate();
c.verdict(false, 25);
sg.cs.setConservation(c);
if (jGroup.getId() != null && groupAnnotRefs.size() > 0)
{
// re-instate unique group/annotation row reference
- List<AlignmentAnnotation> jaal = groupAnnotRefs.get(jGroup
- .getId());
+ List<AlignmentAnnotation> jaal = groupAnnotRefs
+ .get(jGroup.getId());
if (jaal != null)
{
for (AlignmentAnnotation jaa : jaal)
// to the same sequenceSet. We must modify this id on load
// so that each load of the file gives a unique id
String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
- String viewId = (view.getId() == null ? null : view.getId()
- + uniqueSetSuffix);
+ String viewId = (view.getId() == null ? null
+ : view.getId() + uniqueSetSuffix);
AlignFrame af = null;
AlignViewport av = null;
// now check to see if we really need to create a new viewport.
// XML.
// and then recover its containing af to allow the settings to be applied.
// TODO: fix for vamsas demo
- System.err
- .println("About to recover a viewport for existing alignment: Sequence set ID is "
+ System.err.println(
+ "About to recover a viewport for existing alignment: Sequence set ID is "
+ uniqueSeqSetId);
Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
if (seqsetobj != null)
if (seqsetobj instanceof String)
{
uniqueSeqSetId = (String) seqsetobj;
- System.err
- .println("Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
+ System.err.println(
+ "Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
+ uniqueSeqSetId);
}
else
{
- System.err
- .println("Warning : Collision between sequence set ID string and existing jalview object mapping.");
+ System.err.println(
+ "Warning : Collision between sequence set ID string and existing jalview object mapping.");
}
}
* indicate that annotation colours are applied across all groups (pre
* Jalview 2.8.1 behaviour)
*/
- boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan(
- "2.8.1", object.getVersion());
+ boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan("2.8.1",
+ object.getVersion());
AlignmentPanel ap = null;
boolean isnewview = true;
for (int i = 0; i < jseq.getRnaViewerCount(); i++)
{
RnaViewer viewer = jseq.getRnaViewer(i);
- AppVarna appVarna = findOrCreateVarnaViewer(viewer,
- uniqueSetSuffix, ap);
+ AppVarna appVarna = findOrCreateVarnaViewer(viewer, uniqueSetSuffix,
+ ap);
for (int j = 0; j < viewer.getSecondaryStructureCount(); j++)
{
SecondaryStructure ss = viewer.getSecondaryStructure(j);
SequenceI seq = seqRefIds.get(jseq.getId());
- AlignmentAnnotation ann = this.annotationIds.get(ss
- .getAnnotationId());
+ AlignmentAnnotation ann = this.annotationIds
+ .get(ss.getAnnotationId());
/*
* add the structure to the Varna display (with session state copied
/*
* viewer not found - make it
*/
- RnaViewerModel model = new RnaViewerModel(postLoadId,
- viewer.getTitle(), viewer.getXpos(), viewer.getYpos(),
- viewer.getWidth(), viewer.getHeight(),
- viewer.getDividerLocation());
+ RnaViewerModel model = new RnaViewerModel(postLoadId, viewer.getTitle(),
+ viewer.getXpos(), viewer.getYpos(), viewer.getWidth(),
+ viewer.getHeight(), viewer.getDividerLocation());
AppVarna varna = new AppVarna(model, ap);
return varna;
// TODO: should check if tp has been manipulated by user - if so its
// settings shouldn't be modified
tp.setTitle(tree.getTitle());
- tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(), tree
- .getWidth(), tree.getHeight()));
+ tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(),
+ tree.getWidth(), tree.getHeight()));
tp.av = av; // af.viewport; // TODO: verify 'associate with all
// views'
// works still
if (tree.getFontName() != null)
{
- tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
- .getFontStyle(), tree.getFontSize()));
+ tp.setTreeFont(new java.awt.Font(tree.getFontName(),
+ tree.getFontStyle(), tree.getFontSize()));
}
else
{
- tp.setTreeFont(new java.awt.Font(view.getFontName(), view
- .getFontStyle(), tree.getFontSize()));
+ tp.setTreeFont(new java.awt.Font(view.getFontName(),
+ view.getFontStyle(), tree.getFontSize()));
}
tp.showPlaceholders(tree.getMarkUnlinked());
// TODO: NOW: check that this recovers the PDB file correctly.
String pdbFile = loadPDBFile(jprovider, ids[p].getId(),
ids[p].getFile());
- jalview.datamodel.SequenceI seq = seqRefIds.get(jseqs[i]
- .getId() + "");
+ jalview.datamodel.SequenceI seq = seqRefIds
+ .get(jseqs[i].getId() + "");
if (sviewid == null)
{
- sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width
- + "," + height;
+ sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width + ","
+ + height;
}
if (!structureViewers.containsKey(sviewid))
{
// linkAlignPanel,superposeWithAlignpanel}} from hash
StructureViewerModel jmoldat = structureViewers.get(sviewid);
jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel()
- | (structureState.hasAlignwithAlignPanel() ? structureState
- .getAlignwithAlignPanel() : false));
+ | (structureState.hasAlignwithAlignPanel()
+ ? structureState.getAlignwithAlignPanel()
+ : false));
/*
* Default colour by linked panel to false if not specified (e.g.
*/
boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel();
colourWithAlignPanel |= (structureState
- .hasColourwithAlignPanel() ? structureState
- .getColourwithAlignPanel() : false);
+ .hasColourwithAlignPanel()
+ ? structureState.getColourwithAlignPanel()
+ : false);
jmoldat.setColourWithAlignPanel(colourWithAlignPanel);
/*
* pre-2.7 projects)
*/
boolean colourByViewer = jmoldat.isColourByViewer();
- colourByViewer &= structureState.hasColourByJmol() ? structureState
- .getColourByJmol() : true;
+ colourByViewer &= structureState.hasColourByJmol()
+ ? structureState.getColourByJmol()
+ : true;
jmoldat.setColourByViewer(colourByViewer);
if (jmoldat.getStateData().length() < structureState
StructureData seqstrmaps = jmoldat.getFileData().get(mapkey);
if (seqstrmaps == null)
{
- jmoldat.getFileData().put(
- mapkey,
+ jmoldat.getFileData().put(mapkey,
seqstrmaps = jmoldat.new StructureData(pdbFile,
ids[p].getId()));
}
createOrLinkStructureViewer(entry, af, ap, jprovider);
} catch (Exception e)
{
- System.err.println("Error loading structure viewer: "
- + e.getMessage());
+ System.err.println(
+ "Error loading structure viewer: " + e.getMessage());
// failed - try the next one
}
}
// TODO use StructureViewer as a factory here, see JAL-1761
final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs.size()]);
- final SequenceI[][] seqsArray = allseqs.toArray(new SequenceI[allseqs
- .size()][]);
+ final SequenceI[][] seqsArray = allseqs
+ .toArray(new SequenceI[allseqs.size()][]);
String newViewId = viewerData.getKey();
ChimeraViewFrame cvf = new ChimeraViewFrame(chimeraSessionFile,
*/
histbug += 10;
int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", histbug);
- String val = (diff == -1) ? null : newFileLoc
- .substring(histbug, diff);
+ String val = (diff == -1) ? null
+ : newFileLoc.substring(histbug, diff);
if (val != null && val.length() >= 4)
{
if (val.contains("e")) // eh? what can it be?
}
}
- final String[] pdbf = pdbfilenames.toArray(new String[pdbfilenames
- .size()]);
+ final String[] pdbf = pdbfilenames
+ .toArray(new String[pdbfilenames.size()]);
final String[] id = pdbids.toArray(new String[pdbids.size()]);
final SequenceI[][] sq = seqmaps
.toArray(new SequenceI[seqmaps.size()][]);
JalviewStructureDisplayI sview = null;
try
{
- sview = new StructureViewer(alf.alignPanel
- .getStructureSelectionManager()).createView(
- StructureViewer.ViewerType.JMOL, pdbf, id, sq,
- alf.alignPanel, svattrib, fileloc, rect, sviewid);
+ sview = new StructureViewer(
+ alf.alignPanel.getStructureSelectionManager())
+ .createView(StructureViewer.ViewerType.JMOL,
+ pdbf, id, sq, alf.alignPanel, svattrib,
+ fileloc, rect, sviewid);
addNewStructureViewer(sview);
} catch (OutOfMemoryError ex)
{
/*
* Post jalview 2.4 schema includes structure view id
*/
- if (sviewid != null
- && ((StructureViewerBase) frame).getViewId()
- .equals(sviewid))
+ if (sviewid != null && ((StructureViewerBase) frame).getViewId()
+ .equals(sviewid))
{
comp = (StructureViewerBase) frame;
break; // break added in 2.9
for (int i = 0; i < JSEQ.length; i++)
{
- af.viewport.setSequenceColour(af.viewport.getAlignment()
- .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
+ af.viewport.setSequenceColour(
+ af.viewport.getAlignment().getSequenceAt(i),
+ new java.awt.Color(JSEQ[i].getColour()));
}
if (al.hasSeqrep())
for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
{
isRepresentative = true;
- SequenceI sequenceToHide = al.getSequenceAt(JSEQ[s]
- .getHiddenSequences(r));
+ SequenceI sequenceToHide = al
+ .getSequenceAt(JSEQ[s].getHiddenSequences(r));
hidden.addSequence(sequenceToHide, false);
// remove from hiddenSeqs list so we don't try to hide it twice
hiddenSeqs.remove(sequenceToHide);
}
}
- SequenceI[] hseqs = hiddenSeqs.toArray(new SequenceI[hiddenSeqs
- .size()]);
+ SequenceI[] hseqs = hiddenSeqs
+ .toArray(new SequenceI[hiddenSeqs.size()]);
af.viewport.hideSequence(hseqs);
}
af.viewport.setIncrement(view.getConsThreshold());
af.viewport.setShowJVSuffix(view.getShowFullId());
af.viewport.setRightAlignIds(view.getRightAlignIds());
- af.viewport.setFont(
- new java.awt.Font(view.getFontName(), view.getFontStyle(), view
- .getFontSize()), true);
+ af.viewport.setFont(new java.awt.Font(view.getFontName(),
+ view.getFontStyle(), view.getFontSize()), true);
ViewStyleI vs = af.viewport.getViewStyle();
vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna());
af.viewport.setViewStyle(vs);
af.viewport.setTextColour(new java.awt.Color(view.getTextCol1()));
af.viewport.setTextColour2(new java.awt.Color(view.getTextCol2()));
af.viewport.setThresholdTextColour(view.getTextColThreshold());
- af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view
- .isShowUnconserved() : false);
+ af.viewport.setShowUnconserved(
+ view.hasShowUnconserved() ? view.isShowUnconserved() : false);
af.viewport.getRanges().setStartRes(view.getStartRes());
if (view.getViewName() != null)
af.viewport.setGlobalColourScheme(cs);
af.viewport.getResidueShading().setThreshold(view.getPidThreshold(),
view.getIgnoreGapsinConsensus());
- af.viewport.getResidueShading().setConsensus(
- af.viewport.getSequenceConsensusHash());
+ af.viewport.getResidueShading()
+ .setConsensus(af.viewport.getSequenceConsensusHash());
af.viewport.setColourAppliesToAllGroups(false);
if (view.getConservationSelected() && cs != null)
{
- af.viewport.getResidueShading().setConservationInc(
- view.getConsThreshold());
+ af.viewport.getResidueShading()
+ .setConservationInc(view.getConsThreshold());
}
af.changeColour(cs);
}
if (view.hasShowConsensusHistogram())
{
- af.viewport.setShowConsensusHistogram(view
- .getShowConsensusHistogram());
+ af.viewport
+ .setShowConsensusHistogram(view.getShowConsensusHistogram());
}
else
{
Map<String, FeatureColourI> featureColours = new Hashtable<>();
Map<String, Float> featureOrder = new Hashtable<>();
- for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
+ for (int fs = 0; fs < jms.getFeatureSettings()
+ .getSettingCount(); fs++)
{
Setting setting = jms.getFeatureSettings().getSetting(fs);
if (setting.hasMincolour())
{
- FeatureColourI gc = setting.hasMin() ? new FeatureColour(
- new Color(setting.getMincolour()), new Color(
- setting.getColour()), setting.getMin(),
- setting.getMax()) : new FeatureColour(new Color(
- setting.getMincolour()), new Color(setting.getColour()),
- 0, 1);
+ FeatureColourI gc = setting.hasMin()
+ ? new FeatureColour(new Color(setting.getMincolour()),
+ new Color(setting.getColour()), setting.getMin(),
+ setting.getMax())
+ : new FeatureColour(new Color(setting.getMincolour()),
+ new Color(setting.getColour()), 0, 1);
if (setting.hasThreshold())
{
gc.setThreshold(setting.getThreshold());
}
else
{
- featureColours.put(setting.getType(), new FeatureColour(
- new Color(setting.getColour())));
+ featureColours.put(setting.getType(),
+ new FeatureColour(new Color(setting.getColour())));
}
renderOrder[fs] = setting.getType();
if (setting.hasOrder())
}
else
{
- featureOrder.put(setting.getType(), new Float(fs
- / jms.getFeatureSettings().getSettingCount()));
+ featureOrder.put(setting.getType(), new Float(
+ fs / jms.getFeatureSettings().getSettingCount()));
}
if (setting.getDisplay())
{
// FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
// fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
// jms.getFeatureSettings().getTransparency() : 0.0, featureOrder);
- FeatureRendererSettings frs = new FeatureRendererSettings(
- renderOrder, fgtable, featureColours, 1.0f, featureOrder);
+ FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
+ fgtable, featureColours, 1.0f, featureOrder);
af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
.transferSettings(frs);
{
for (int c = 0; c < view.getHiddenColumnsCount(); c++)
{
- af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), view
- .getHiddenColumns(c).getEnd() // +1
- );
+ af.viewport.hideColumns(view.getHiddenColumns(c).getStart(),
+ view.getHiddenColumns(c).getEnd() // +1
+ );
}
}
if (view.getCalcIdParam() != null)
/*
* pre 2.10.2: saved annotationId is AlignmentAnnotation.label
*/
- if (matchedAnnotation == null && annAlignment.getAlignmentAnnotation() != null)
+ if (matchedAnnotation == null
+ && annAlignment.getAlignmentAnnotation() != null)
{
for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
{
}
if (matchedAnnotation.getThreshold() == null)
{
- matchedAnnotation.setThreshold(new GraphLine(viewAnnColour.getThreshold(),
- "Threshold", Color.black));
+ matchedAnnotation.setThreshold(new GraphLine(
+ viewAnnColour.getThreshold(), "Threshold", Color.black));
}
AnnotationColourGradient cs = null;
if (viewAnnColour.getColourScheme().equals("None"))
{
- cs = new AnnotationColourGradient(matchedAnnotation, new Color(
- viewAnnColour.getMinColour()), new Color(
- viewAnnColour.getMaxColour()),
+ cs = new AnnotationColourGradient(matchedAnnotation,
+ new Color(viewAnnColour.getMinColour()),
+ new Color(viewAnnColour.getMaxColour()),
viewAnnColour.getAboveThreshold());
}
else if (viewAnnColour.getColourScheme().startsWith("ucs"))
{
- cs = new AnnotationColourGradient(matchedAnnotation, getUserColourScheme(
- jms, viewAnnColour.getColourScheme()),
+ cs = new AnnotationColourGradient(matchedAnnotation,
+ getUserColourScheme(jms, viewAnnColour.getColourScheme()),
viewAnnColour.getAboveThreshold());
}
else
for (JvAnnotRow auan : autoAlan)
{
visan.put(auan.template.label
- + (auan.template.getCalcId() == null ? "" : "\t"
- + auan.template.getCalcId()), auan);
+ + (auan.template.getCalcId() == null ? ""
+ : "\t" + auan.template.getCalcId()),
+ auan);
}
int hSize = al.getAlignmentAnnotation().length;
List<JvAnnotRow> reorder = new ArrayList<>();
return false;
}
String id;
- if (skipList.containsKey(id = object.getJalviewModelSequence()
- .getViewport()[0].getSequenceSetId()))
+ if (skipList.containsKey(
+ id = object.getJalviewModelSequence().getViewport()[0]
+ .getSequenceSetId()))
{
if (Cache.log != null && Cache.log.isDebugEnabled())
{
private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al,
boolean ignoreUnrefed)
{
- jalview.datamodel.AlignmentI ds = getDatasetFor(vamsasSet
- .getDatasetId());
+ jalview.datamodel.AlignmentI ds = getDatasetFor(
+ vamsasSet.getDatasetId());
Vector dseqs = null;
if (ds == null)
{
}
// TODO: merges will never happen if we 'know' we have the real dataset
// sequence - this should be detected when id==dssid
- System.err
- .println("DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
+ System.err.println(
+ "DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
// + (pre ? "prepended" : "") + " "
// + (post ? "appended" : ""));
}
{
DBRef dr = sequence.getDBRef(d);
jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
- sequence.getDBRef(d).getSource(), sequence.getDBRef(d)
- .getVersion(), sequence.getDBRef(d).getAccessionId());
+ sequence.getDBRef(d).getSource(),
+ sequence.getDBRef(d).getVersion(),
+ sequence.getDBRef(d).getAccessionId());
if (dr.getMapping() != null)
{
entry.setMap(addMapping(dr.getMapping()));
fto[_i] = mf.getStart();
fto[_i + 1] = mf.getEnd();
}
- jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto,
- fr, fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit());
+ jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, fr,
+ fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit());
if (m.getMappingChoice() != null)
{
MappingChoice mc = m.getMappingChoice();
}
else
{
- System.err
- .println("Warning - making up dataset sequence id for DbRef sequence map reference");
+ System.err.println(
+ "Warning - making up dataset sequence id for DbRef sequence map reference");
sqid = ((Object) ms).toString(); // make up a new hascode for
// undefined dataset sequence hash
// (unlikely to happen)
for (int i = 0; i < csize; i++)
{
- newColours[i] = new java.awt.Color(Integer.parseInt(colours
- .getUserColourScheme().getColour(i).getRGB(), 16));
+ newColours[i] = new java.awt.Color(Integer.parseInt(
+ colours.getUserColourScheme().getColour(i).getRGB(), 16));
}
return new jalview.schemes.UserColourScheme(newColours);
public void run()
{
- System.err.println("Couldn't locate Jalview XML file : " + ex
- + "\n");
+ System.err.println(
+ "Couldn't locate Jalview XML file : " + ex + "\n");
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.formatMessage("label.couldnt_locate",
- new String[] { file }), MessageManager
- .getString("label.url_not_found"),
+ new String[]
+ { file }),
+ MessageManager.getString("label.url_not_found"),
JvOptionPane.WARNING_MESSAGE);
}
});
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.formatMessage(
"label.error_loading_file_params", new String[]
- { file }), MessageManager
+ { file }),
+ MessageManager
.getString("label.error_loading_jalview_file"),
JvOptionPane.WARNING_MESSAGE);
}
}
}
al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
- StructureSelectionManager.getStructureSelectionManager(
- Desktop.instance).registerPDBEntry(entry);
+ StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance)
+ .registerPDBEntry(entry);
}
}
for (int i = 0; i < JSEQ.length; i++)
{
- af.viewport.setSequenceColour(af.viewport.getAlignment()
- .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
+ af.viewport.setSequenceColour(
+ af.viewport.getAlignment().getSequenceAt(i),
+ new java.awt.Color(JSEQ[i].getColour()));
}
// af.changeColour() );
}
else
{
- cs = ColourSchemeProperty.getColourScheme(al, groups[i].getColour());
+ cs = ColourSchemeProperty.getColourScheme(al,
+ groups[i].getColour());
}
}
int pidThreshold = groups[i].getPidThreshold();
groups[i].getStart(), groups[i].getEnd());
sg.getGroupColourScheme().setThreshold(pidThreshold, true);
- sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));
+ sg.setOutlineColour(
+ new java.awt.Color(groups[i].getOutlineColour()));
if (groups[i].getConsThreshold() != 0)
{
- Conservation c = new Conservation("All", sg.getSequences(null),
- 0, sg.getWidth() - 1);
+ Conservation c = new Conservation("All", sg.getSequences(null), 0,
+ sg.getWidth() - 1);
c.calculate();
c.verdict(false, 25);
sg.cs.setConservation(c);
af.viewport.setColourText(view.getShowColourText());
af.viewport.setConservationSelected(view.getConservationSelected());
af.viewport.setShowJVSuffix(view.getShowFullId());
- af.viewport.setFont(
- new java.awt.Font(view.getFontName(), view.getFontStyle(), view
- .getFontSize()), true);
+ af.viewport.setFont(new java.awt.Font(view.getFontName(),
+ view.getFontStyle(), view.getFontSize()), true);
af.viewport.setRenderGaps(view.getRenderGaps());
af.viewport.setWrapAlignment(view.getWrapAlignment());
// }
}
- af.viewport.getResidueShading().setThreshold(
- view.getPidThreshold(), true);
- af.viewport.getResidueShading().setConsensus(
- af.viewport.getSequenceConsensusHash());
+ af.viewport.getResidueShading().setThreshold(view.getPidThreshold(),
+ true);
+ af.viewport.getResidueShading()
+ .setConsensus(af.viewport.getSequenceConsensusHash());
af.viewport.setColourAppliesToAllGroups(false);
af.alignPanel.updateLayout();
af.changeColour(cs);
if (view.getConservationSelected() && cs != null)
{
- af.viewport.getResidueShading().setConservationInc(
- view.getConsThreshold());
+ af.viewport.getResidueShading()
+ .setConservationInc(view.getConsThreshold());
}
af.viewport.setColourAppliesToAllGroups(true);
Hashtable featureColours = new Hashtable();
String[] renderOrder = new String[jms.getFeatureSettings()
.getSettingCount()];
- for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
+ for (int fs = 0; fs < jms.getFeatureSettings()
+ .getSettingCount(); fs++)
{
Setting setting = jms.getFeatureSettings().getSetting(fs);
new Integer(setting.getColour()));
}
}
- FeatureRendererSettings frs = new FeatureRendererSettings(
- renderOrder, new Hashtable(), featureColours, 1.0f, null);
+ FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
+ new Hashtable(), featureColours, 1.0f, null);
af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
.transferSettings(frs);
}
if (tree.getFontName() != null)
{
- tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
- .getFontStyle(), tree.getFontSize()));
+ tp.setTreeFont(new java.awt.Font(tree.getFontName(),
+ tree.getFontStyle(), tree.getFontSize()));
}
else
{
- tp.setTreeFont(new java.awt.Font(view.getFontName(), view
- .getFontStyle(), tree.getFontSize()));
+ tp.setTreeFont(new java.awt.Font(view.getFontName(),
+ view.getFontStyle(), tree.getFontSize()));
}
tp.showPlaceholders(tree.getMarkUnlinked());
protected void sendAsynchronousCommand(final String command,
final String progressMsg)
{
- final long handle = progressMsg == null ? 0 : cvf
- .startProgressBar(progressMsg);
+ final long handle = progressMsg == null ? 0
+ : cvf.startProgressBar(progressMsg);
SwingUtilities.invokeLater(new Runnable()
{
@Override
public static int showConfirmDialog(Component parentComponent,
Object message) throws HeadlessException
{
- return isInteractiveMode() ? JOptionPane.showConfirmDialog(
- parentComponent, message) : (int) getMockResponse();
+ return isInteractiveMode()
+ ? JOptionPane.showConfirmDialog(parentComponent, message)
+ : (int) getMockResponse();
}
public static int showConfirmDialog(Component parentComponent,
Object message, String title, int optionType)
throws HeadlessException
{
- return isInteractiveMode() ? JOptionPane.showConfirmDialog(
- parentComponent, message, title, optionType)
+ return isInteractiveMode()
+ ? JOptionPane.showConfirmDialog(parentComponent, message, title,
+ optionType)
: (int) getMockResponse();
}
Object message, String title, int optionType, int messageType)
throws HeadlessException
{
- return isInteractiveMode() ? JOptionPane.showConfirmDialog(
- parentComponent, message, title, optionType, messageType)
+ return isInteractiveMode()
+ ? JOptionPane.showConfirmDialog(parentComponent, message, title,
+ optionType, messageType)
: (int) getMockResponse();
}
Object message, String title, int optionType, int messageType,
Icon icon) throws HeadlessException
{
- return isInteractiveMode() ? JOptionPane.showConfirmDialog(
- parentComponent, message, title, optionType, messageType, icon)
+ return isInteractiveMode()
+ ? JOptionPane.showConfirmDialog(parentComponent, message, title,
+ optionType, messageType, icon)
: (int) getMockResponse();
}
public static int showInternalConfirmDialog(Component parentComponent,
Object message)
{
- return isInteractiveMode() ? JOptionPane.showInternalConfirmDialog(
- parentComponent, message) : (int) getMockResponse();
+ return isInteractiveMode()
+ ? JOptionPane.showInternalConfirmDialog(parentComponent,
+ message)
+ : (int) getMockResponse();
}
public static int showInternalConfirmDialog(Component parentComponent,
Object message, String title, int optionType)
{
- return isInteractiveMode() ? JOptionPane.showConfirmDialog(
- parentComponent, message, title, optionType)
+ return isInteractiveMode()
+ ? JOptionPane.showConfirmDialog(parentComponent, message, title,
+ optionType)
: (int) getMockResponse();
}
public static int showInternalConfirmDialog(Component parentComponent,
Object message, String title, int optionType, int messageType)
{
- return isInteractiveMode() ? JOptionPane.showConfirmDialog(
- parentComponent, message, title, optionType, messageType)
+ return isInteractiveMode()
+ ? JOptionPane.showConfirmDialog(parentComponent, message, title,
+ optionType, messageType)
: (int) getMockResponse();
}
Object message, String title, int optionType, int messageType,
Icon icon)
{
- return isInteractiveMode() ? JOptionPane.showInternalConfirmDialog(
- parentComponent, message, title, optionType, messageType, icon)
+ return isInteractiveMode()
+ ? JOptionPane.showInternalConfirmDialog(parentComponent,
+ message, title, optionType, messageType, icon)
: (int) getMockResponse();
}
Icon icon, Object[] options, Object initialValue)
throws HeadlessException
{
- return isInteractiveMode() ? JOptionPane.showOptionDialog(
- parentComponent, message, title, optionType, messageType, icon,
- options, initialValue) : (int) getMockResponse();
+ return isInteractiveMode()
+ ? JOptionPane.showOptionDialog(parentComponent, message, title,
+ optionType, messageType, icon, options, initialValue)
+ : (int) getMockResponse();
}
public static void showMessageDialog(Component parentComponent,
public static String showInputDialog(Object message,
Object initialSelectionValue)
{
- return isInteractiveMode() ? JOptionPane.showInputDialog(message,
- initialSelectionValue) : getMockResponse().toString();
+ return isInteractiveMode()
+ ? JOptionPane.showInputDialog(message, initialSelectionValue)
+ : getMockResponse().toString();
}
public static String showInputDialog(Component parentComponent,
Object message) throws HeadlessException
{
- return isInteractiveMode() ? JOptionPane.showInputDialog(
- parentComponent, message) : getMockResponse().toString();
+ return isInteractiveMode()
+ ? JOptionPane.showInputDialog(parentComponent, message)
+ : getMockResponse().toString();
}
public static String showInputDialog(Component parentComponent,
Object message, Object initialSelectionValue)
{
- return isInteractiveMode() ? JOptionPane.showInputDialog(
- parentComponent, message, initialSelectionValue)
+ return isInteractiveMode()
+ ? JOptionPane.showInputDialog(parentComponent, message,
+ initialSelectionValue)
: getMockResponse().toString();
}
Object message, String title, int messageType)
throws HeadlessException
{
- return isInteractiveMode() ? JOptionPane.showInputDialog(
- parentComponent, message, title, messageType)
+ return isInteractiveMode()
+ ? JOptionPane.showInputDialog(parentComponent, message, title,
+ messageType)
: getMockResponse().toString();
}
Object[] selectionValues, Object initialSelectionValue)
throws HeadlessException
{
- return isInteractiveMode() ? JOptionPane.showInputDialog(
- parentComponent, message, title, messageType, icon,
- selectionValues, initialSelectionValue) : getMockResponse()
- .toString();
+ return isInteractiveMode()
+ ? JOptionPane.showInputDialog(parentComponent, message, title,
+ messageType, icon, selectionValues,
+ initialSelectionValue)
+ : getMockResponse().toString();
}
public static String showInternalInputDialog(Component parentComponent,
Object message)
{
- return isInteractiveMode() ? JOptionPane.showInternalInputDialog(
- parentComponent, message) : getMockResponse().toString();
+ return isInteractiveMode()
+ ? JOptionPane.showInternalInputDialog(parentComponent, message)
+ : getMockResponse().toString();
}
public static String showInternalInputDialog(Component parentComponent,
Object message, String title, int messageType)
{
- return isInteractiveMode() ? JOptionPane.showInternalInputDialog(
- parentComponent, message, title, messageType)
+ return isInteractiveMode()
+ ? JOptionPane.showInternalInputDialog(parentComponent, message,
+ title, messageType)
: getMockResponse().toString();
}
Object message, String title, int messageType, Icon icon,
Object[] selectionValues, Object initialSelectionValue)
{
- return isInteractiveMode() ? JOptionPane.showInternalInputDialog(
- parentComponent, message, title, messageType, icon,
- selectionValues, initialSelectionValue) : getMockResponse()
- .toString();
+ return isInteractiveMode()
+ ? JOptionPane.showInternalInputDialog(parentComponent, message,
+ title, messageType, icon, selectionValues,
+ initialSelectionValue)
+ : getMockResponse().toString();
}
private static void outputMessage(Object message)
*/
public static String wrapTooltip(boolean enclose, String ttext)
{
- Objects.requireNonNull(ttext, "Tootip text to format must not be null!");
+ Objects.requireNonNull(ttext,
+ "Tootip text to format must not be null!");
ttext = ttext.trim();
boolean maxLengthExceeded = false;
for (int i = 0, iSize = menu.getMenuComponentCount(); i < iSize; i++)
{
if (menu.getMenuComponent(i) instanceof JMenu
- && ((JMenu) menu.getMenuComponent(i)).getText().equals(
- submenu))
+ && ((JMenu) menu.getMenuComponent(i)).getText()
+ .equals(submenu))
{
submenuinstance = (JMenu) menu.getMenuComponent(i);
}
public static Font getLabelFont(boolean bold, boolean italic)
{
- return new java.awt.Font("Verdana", (!bold && !italic) ? Font.PLAIN
- : (bold ? Font.BOLD : 0) + (italic ? Font.ITALIC : 0), 11);
+ return new java.awt.Font("Verdana",
+ (!bold && !italic) ? Font.PLAIN
+ : (bold ? Font.BOLD : 0) + (italic ? Font.ITALIC : 0),
+ 11);
}
/**
* of possible positions.
*/
float fraction = proportion
- * (scrollbar.getMaximum() - scrollbar.getMinimum() - scrollbar
- .getModel().getExtent())
+ * (scrollbar.getMaximum() - scrollbar.getMinimum()
+ - scrollbar.getModel().getExtent())
+ (scrollbar.getModel().getExtent() / 2f);
return Math.min(Math.round(fraction), scrollbar.getMaximum());
}
{
if (jalview.bin.Cache.log != null)
{
- jalview.bin.Cache.log
- .error("Out of Memory when " + action, oomex);
+ jalview.bin.Cache.log.error("Out of Memory when " + action,
+ oomex);
}
else
{
@Override
public void run()
{
- JvOptionPane
- .showInternalMessageDialog(desktop,
- MessageManager.formatMessage("warn.out_of_memory_when_action",
- new String[] { action }), MessageManager
- .getString("label.out_of_memory"),
- JvOptionPane.WARNING_MESSAGE);
+ JvOptionPane.showInternalMessageDialog(desktop, MessageManager
+ .formatMessage("warn.out_of_memory_when_action", new String[]
+ { action }), MessageManager.getString("label.out_of_memory"),
+ JvOptionPane.WARNING_MESSAGE);
// hope that there's enough memory left that no more appear.
oomInprogress = false;
}
*/
boolean compact = false;
- public class OptionBox extends JPanel implements MouseListener,
- ActionListener
+ public class OptionBox extends JPanel
+ implements MouseListener, ActionListener
{
JCheckBox enabled = new JCheckBox();
{
hasLink = true;
- enabled.setToolTipText(JvSwingUtils
- .wrapTooltip(
- true,
- ((desc == null || desc.trim().length() == 0) ? MessageManager
- .getString("label.opt_and_params_further_details")
- : desc)
- + "<br><img src=\"" + linkImageURL + "\"/>"));
+ enabled.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ ((desc == null || desc.trim().length() == 0)
+ ? MessageManager.getString(
+ "label.opt_and_params_further_details")
+ : desc) + "<br><img src=\"" + linkImageURL
+ + "\"/>"));
enabled.addMouseListener(this);
}
else
{
if (desc != null && desc.trim().length() > 0)
{
- enabled.setToolTipText(JvSwingUtils.wrapTooltip(true,
- opt.getDescription()));
+ enabled.setToolTipText(
+ JvSwingUtils.wrapTooltip(true, opt.getDescription()));
}
}
add(enabled, BorderLayout.NORTH);
}
- public class ParamBox extends JPanel implements ChangeListener,
- ActionListener, MouseListener
+ public class ParamBox extends JPanel
+ implements ChangeListener, ActionListener, MouseListener
{
boolean adjusting = false;
JTextField valueField = null;
- public ParamBox(final OptsParametersContainerI pmlayout, ParameterI parm)
+ public ParamBox(final OptsParametersContainerI pmlayout,
+ ParameterI parm)
{
pmdialogbox = pmlayout;
finfo = parm.getFurtherDetails();
&& parm.getDescription().trim().length() > 0)
{
// Only create description boxes if there actually is a description.
- ttipText = (JvSwingUtils
- .wrapTooltip(
- true,
- parm.getDescription()
- + (finfo != null ? "<br><img src=\""
- + linkImageURL
- + "\"/>"
- + MessageManager
- .getString("label.opt_and_params_further_details")
- : "")));
- }
-
- JvSwingUtils.mgAddtoLayout(this, ttipText,
- new JLabel(parm.getName()), controlPanel, "");
+ ttipText = (JvSwingUtils.wrapTooltip(true,
+ parm.getDescription() + (finfo != null ? "<br><img src=\""
+ + linkImageURL + "\"/>"
+ + MessageManager.getString(
+ "label.opt_and_params_further_details")
+ : "")));
+ }
+
+ JvSwingUtils.mgAddtoLayout(this, ttipText, new JLabel(parm.getName()),
+ controlPanel, "");
updateControls(parm);
validate();
}
// Only create description boxes if there actually is a description.
if (finfo != null)
{
- showDesc.setToolTipText(JvSwingUtils.wrapTooltip(
- true,
- MessageManager
- .formatMessage(
- "label.opt_and_params_show_brief_desc_image_link",
- new String[] { linkImageURL
- .toExternalForm() })));
+ showDesc.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager.formatMessage(
+ "label.opt_and_params_show_brief_desc_image_link",
+ new String[]
+ { linkImageURL.toExternalForm() })));
showDesc.addMouseListener(this);
}
else
{
- showDesc.setToolTipText(JvSwingUtils.wrapTooltip(
- true,
- MessageManager
- .getString("label.opt_and_params_show_brief_desc")));
+ showDesc.setToolTipText(
+ JvSwingUtils.wrapTooltip(true, MessageManager.getString(
+ "label.opt_and_params_show_brief_desc")));
}
showDesc.addActionListener(new ActionListener()
{
{
if (!adjusting)
{
- valueField.setText(""
- + ((integ) ? ("" + slider.getValue()) : ("" + slider
- .getValue() / 1000f)));
+ valueField.setText("" + ((integ) ? ("" + slider.getValue())
+ : ("" + slider.getValue() / 1000f)));
checkIfModified();
}
{
JPopupMenu mnu = new JPopupMenu();
- JMenuItem mitem = new JMenuItem(MessageManager.formatMessage(
- "label.view_params", new String[] { finfo }));
+ JMenuItem mitem = new JMenuItem(
+ MessageManager.formatMessage("label.view_params", new String[]
+ { finfo }));
mitem.addActionListener(new ActionListener()
{
else
{
throw new Error(MessageManager.formatMessage(
- "error.invalid_value_for_option", new String[] { string,
- option.getName() }));
+ "error.invalid_value_for_option", new String[]
+ { string, option.getName() }));
}
}
* @author $author$
* @version $Revision$
*/
-public class OverviewPanel extends JPanel implements Runnable,
- ViewportListenerI
+public class OverviewPanel extends JPanel
+ implements Runnable, ViewportListenerI
{
private OverviewDimensions od;
this.ap = alPanel;
od = new OverviewDimensionsShowHidden(av.getRanges(),
- (av.isShowAnnotation() && av
- .getAlignmentConservationAnnotation() != null));
+ (av.isShowAnnotation()
+ && av.getAlignmentConservationAnnotation() != null));
setSize(od.getWidth(), od.getHeight());
{
// set the mouse position as a fixed point in the box
// and drag relative to that position
- od.adjustViewportFromMouse(evt.getX(),
- evt.getY(), av.getAlignment().getHiddenSequences(),
+ od.adjustViewportFromMouse(evt.getX(), evt.getY(),
+ av.getAlignment().getHiddenSequences(),
av.getAlignment().getHiddenColumns());
}
else
{
- od.updateViewportFromMouse(evt.getX(), evt.getY(), av
- .getAlignment().getHiddenSequences(), av.getAlignment()
- .getHiddenColumns());
+ od.updateViewportFromMouse(evt.getX(), evt.getY(),
+ av.getAlignment().getHiddenSequences(),
+ av.getAlignment().getHiddenColumns());
}
}
}
{
showHidden = false;
od = new OverviewDimensionsHideHidden(av.getRanges(),
- (av.isShowAnnotation() && av
- .getAlignmentConservationAnnotation() != null));
+ (av.isShowAnnotation()
+ && av.getAlignmentConservationAnnotation() != null));
}
else
{
showHidden = true;
od = new OverviewDimensionsShowHidden(av.getRanges(),
- (av.isShowAnnotation() && av
- .getAlignmentConservationAnnotation() != null));
+ (av.isShowAnnotation()
+ && av.getAlignmentConservationAnnotation() != null));
}
oviewCanvas.resetOviewDims(od);
updateOverviewImage();
od.setWidth(getWidth());
od.setHeight(getHeight());
}
-
+
setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
if (oviewCanvas.restartDraw())
public void run()
{
oviewCanvas.draw(av.isShowSequenceFeatures(),
- (av.isShowAnnotation() && av
- .getAlignmentConservationAnnotation() != null), ap
- .getSeqPanel().seqCanvas.getFeatureRenderer());
+ (av.isShowAnnotation()
+ && av.getAlignmentConservationAnnotation() != null),
+ ap.getSeqPanel().seqCanvas.getFeatureRenderer());
setBoxPosition();
}
*/
private void setBoxPosition()
{
- od.setBoxPosition(av.getAlignment().getHiddenSequences(), av
- .getAlignment().getHiddenColumns());
+ od.setBoxPosition(av.getAlignment().getHiddenSequences(),
+ av.getAlignment().getHiddenColumns());
repaint();
}
* @author $author$
* @version $Revision$
*/
-public class PCAPanel extends GPCAPanel implements Runnable,
- IProgressIndicator
+public class PCAPanel extends GPCAPanel
+ implements Runnable, IProgressIndicator
{
private IProgressIndicator progressBar;
*/
public PCAPanel(AlignmentPanel alignPanel)
{
- this(alignPanel, ScoreModels.getInstance()
- .getDefaultModel(!alignPanel.av.getAlignment().isNucleotide())
- .getName(), SimilarityParams.SeqSpace);
+ this(alignPanel,
+ ScoreModels.getInstance()
+ .getDefaultModel(
+ !alignPanel.av.getAlignment().isNucleotide())
+ .getName(),
+ SimilarityParams.SeqSpace);
}
/**
seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
}
- ScoreModelI scoreModel = ScoreModels.getInstance().getScoreModel(
- modelName, ap);
+ ScoreModelI scoreModel = ScoreModels.getInstance()
+ .getScoreModel(modelName, ap);
pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
params);
PaintRefresher.Register(this, av.getSequenceSetId());
{
if (!pcaModel.getScoreModelName().equals(name))
{
- ScoreModelI sm2 = ScoreModels.getInstance().getScoreModel(
- name, ap);
+ ScoreModelI sm2 = ScoreModels.getInstance()
+ .getScoreModel(name, ap);
pcaModel.setScoreModel(sm2);
Thread worker = new Thread(PCAPanel.this);
worker.start();
if (!pcaModel.isNucleotide())
{
pcaModel.setNucleotide(true);
- pcaModel.setScoreModel(ScoreModels.getInstance().getDefaultModel(
- false));
+ pcaModel.setScoreModel(
+ ScoreModels.getInstance().getDefaultModel(false));
Thread worker = new Thread(this);
worker.start();
}
if (pcaModel.isNucleotide())
{
pcaModel.setNucleotide(false);
- pcaModel.setScoreModel(ScoreModels.getInstance()
- .getDefaultModel(true));
+ pcaModel.setScoreModel(
+ ScoreModels.getInstance().getDefaultModel(true));
Thread worker = new Thread(this);
worker.start();
}
// make this an abstract function of all jalview analysis windows
if (pcaModel.getSeqtrings() == null)
{
- jalview.bin.Cache.log
- .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
+ jalview.bin.Cache.log.info(
+ "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
return;
}
// decide if av alignment is sufficiently different to original data to
// AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
- AlignmentI dataset = (av != null && av.getAlignment() != null) ? av
- .getAlignment().getDataset() : null;
+ AlignmentI dataset = (av != null && av.getAlignment() != null)
+ ? av.getAlignment().getDataset()
+ : null;
if (dataset != null)
{
al.setDataset(dataset);
{
// make a new frame!
AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
// >>>This is a fix for the moment, until a better solution is
// found!!<<<
// msaorder);
Desktop.addInternalFrame(af, MessageManager.formatMessage(
- "label.original_data_for_params",
- new String[] { this.title }), AlignFrame.DEFAULT_WIDTH,
+ "label.original_data_for_params", new String[]
+ { this.title }), AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
}
}
void buildAssociatedViewMenu()
{
- AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
- .getSequenceSetId());
+ AlignmentPanel[] aps = PaintRefresher
+ .getAssociatedPanels(av.getSequenceSetId());
if (aps.length == 1 && rc.av == aps[0].av)
{
associateViewsMenu.setVisible(false);
associateViewsMenu.setVisible(true);
- if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
+ if ((viewMenu
+ .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
{
viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
}
associateViewsMenu.add(item);
}
- final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
+ final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
+ "All Views");
buttonGroup.add(itemf);
cap.setText(pcaModel.getPointsasCsv(false,
xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
zCombobox.getSelectedIndex()));
- Desktop.addInternalFrame(cap, MessageManager.formatMessage(
- "label.points_for_params", new String[] { this.getTitle() }),
- 500, 500);
+ Desktop.addInternalFrame(cap, MessageManager
+ .formatMessage("label.points_for_params", new String[]
+ { this.getTitle() }), 500, 500);
} catch (OutOfMemoryError oom)
{
new OOMWarning("exporting PCA points", oom);
xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
zCombobox.getSelectedIndex()));
Desktop.addInternalFrame(cap, MessageManager.formatMessage(
- "label.transformed_points_for_params",
- new String[] { this.getTitle() }), 500, 500);
+ "label.transformed_points_for_params", new String[]
+ { this.getTitle() }), 500, 500);
} catch (OutOfMemoryError oom)
{
new OOMWarning("exporting transformed PCA points", oom);
{
// raise an implementation warning here - not sure if this situation
// will ever occur
- System.err
- .println("IMPLEMENTATION PROBLEM: DATASET out of sync due to an insert whilst calling PaintRefresher.validateSequences(AlignmentI, ALignmentI)");
+ System.err.println(
+ "IMPLEMENTATION PROBLEM: DATASET out of sync due to an insert whilst calling PaintRefresher.validateSequences(AlignmentI, ALignmentI)");
}
List<SequenceI> alsq;
synchronized (alsq = comp.getSequences())
if (count > 2)
{
- System.out
- .println("Pairwise alignment scaled similarity score matrix\n");
+ System.out.println(
+ "Pairwise alignment scaled similarity score matrix\n");
for (int i = 0; i < count; i++)
{
- jalview.util.Format.print(System.out, "%s \n", ("" + i) + " "
- + seqs[i].getName());
+ jalview.util.Format.print(System.out, "%s \n",
+ ("" + i) + " " + seqs[i].getName());
}
System.out.println("\n");
{
for (int j = 0; j < i; j++)
{
- jalview.util.Format.print(System.out, "%7.3f", scores[i][j]
- / totscore);
+ jalview.util.Format.print(System.out, "%7.3f",
+ scores[i][j] / totscore);
}
}
* @param seq
* DOCUMENT ME!
*/
- public PopupMenu(final AlignmentPanel ap, Sequence seq, List<String> links)
+ public PopupMenu(final AlignmentPanel ap, Sequence seq,
+ List<String> links)
{
this(ap, seq, links, null);
}
* 'reference annotations' that may be added to the alignment. First for the
* currently selected sequence (if there is one):
*/
- final List<SequenceI> selectedSequence = (seq == null ? Collections
- .<SequenceI> emptyList() : Arrays.asList(seq));
+ final List<SequenceI> selectedSequence = (seq == null
+ ? Collections.<SequenceI> emptyList()
+ : Arrays.asList(seq));
buildAnnotationTypesMenus(seqShowAnnotationsMenu,
seqHideAnnotationsMenu, selectedSequence);
configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
/*
* And repeat for the current selection group (if there is one):
*/
- final List<SequenceI> selectedGroup = (ap.av.getSelectionGroup() == null ? Collections
- .<SequenceI> emptyList() : ap.av.getSelectionGroup()
- .getSequences());
+ final List<SequenceI> selectedGroup = (ap.av.getSelectionGroup() == null
+ ? Collections.<SequenceI> emptyList()
+ : ap.av.getSelectionGroup().getSequences());
buildAnnotationTypesMenus(groupShowAnnotationsMenu,
groupHideAnnotationsMenu, selectedGroup);
configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
sequenceMenu.setText(sequence.getName());
if (seq == ap.av.getAlignment().getSeqrep())
{
- makeReferenceSeq.setText(MessageManager
- .getString("action.unmark_as_reference"));
+ makeReferenceSeq.setText(
+ MessageManager.getString("action.unmark_as_reference"));
}
else
{
- makeReferenceSeq.setText(MessageManager
- .getString("action.set_as_reference"));
+ makeReferenceSeq.setText(
+ MessageManager.getString("action.set_as_reference"));
}
if (!ap.av.getAlignment().isNucleotide())
*/
menuItem = new JMenuItem();
menuItem.setText(MessageManager.formatMessage(
- "label.2d_rna_structure_line",
- new Object[] { aa.label }));
+ "label.2d_rna_structure_line", new Object[]
+ { aa.label }));
menuItem.addActionListener(new ActionListener()
{
@Override
// TODO: make rnastrucF a bit more nice
menuItem = new JMenuItem();
menuItem.setText(MessageManager.formatMessage(
- "label.2d_rna_sequence_name",
- new Object[] { seq.getName() }));
+ "label.2d_rna_sequence_name", new Object[]
+ { seq.getName() }));
menuItem.addActionListener(new ActionListener()
{
@Override
if (ap.av.getSelectionGroup() != null
&& ap.av.getSelectionGroup().getSize() > 1)
{
- menuItem = new JMenuItem(MessageManager.formatMessage(
- "label.represent_group_with",
- new Object[] { seq.getName() }));
+ menuItem = new JMenuItem(MessageManager
+ .formatMessage("label.represent_group_with", new Object[]
+ { seq.getName() }));
menuItem.addActionListener(new ActionListener()
{
@Override
}
SequenceGroup sg = ap.av.getSelectionGroup();
- boolean isDefinedGroup = (sg != null) ? ap.av.getAlignment()
- .getGroups().contains(sg) : false;
+ boolean isDefinedGroup = (sg != null)
+ ? ap.av.getAlignment().getGroups().contains(sg)
+ : false;
if (sg != null && sg.getSize() > 0)
{
buildGroupURLMenu(sg, groupLinks);
}
// Add a 'show all structures' for the current selection
- Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>(), reppdb = new Hashtable<String, PDBEntry>();
+ Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>(),
+ reppdb = new Hashtable<String, PDBEntry>();
SequenceI sqass = null;
for (SequenceI sq : ap.av.getSequenceSelection())
{
}
if (pdbe.size() > 0)
{
- final PDBEntry[] pe = pdbe.values().toArray(
- new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray(
- new PDBEntry[reppdb.size()]);
+ final PDBEntry[] pe = pdbe.values()
+ .toArray(new PDBEntry[pdbe.size()]),
+ pr = reppdb.values().toArray(new PDBEntry[reppdb.size()]);
final JMenuItem gpdbview, rpdbview;
}
}
showMenu.removeAll();
hideMenu.removeAll();
- final List<String> all = Arrays.asList(new String[] { MessageManager
- .getString("label.all") });
- addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
+ final List<String> all = Arrays
+ .asList(new String[]
+ { MessageManager.getString("label.all") });
+ addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true,
+ true);
addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
false);
showMenu.addSeparator();
for (int sq = 0; sq < seqs.length; sq++)
{
- int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
- .findPosition(sg.getEndRes());
+ int start = seqs[sq].findPosition(sg.getStartRes()),
+ end = seqs[sq].findPosition(sg.getEndRes());
// just collect ids from dataset sequence
// TODO: check if IDs collected from selecton group intersects with the
// current selection, too
if (((String[]) sarray[1])[sq] == null)
{
- if (!dbr[d].hasMap()
- || (dbr[d].getMap().locateMappedRange(start, end) != null))
+ if (!dbr[d].hasMap() || (dbr[d].getMap()
+ .locateMappedRange(start, end) != null))
{
((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
((int[]) sarray[0])[0]++;
int type = urlLink.getGroupURLType() & 3;
// first two bits ofurlLink type bitfield are sequenceids and sequences
// TODO: FUTURE: ensure the groupURL menu structure can be generalised
- addshowLink(linkMenus[type], label
- + (((type & 1) == 1) ? ("("
- + (usingNames ? "Names" : ltarget) + ")") : ""),
+ addshowLink(linkMenus[type],
+ label + (((type & 1) == 1)
+ ? ("(" + (usingNames ? "Names" : ltarget) + ")")
+ : ""),
urlLink, urlset);
addMenu = true;
}
}
}
- private void addshowLinks(JMenu linkMenu, Collection<List<String>> linkset)
+ private void addshowLinks(JMenu linkMenu,
+ Collection<List<String>> linkset)
{
for (List<String> linkstrset : linkset)
{
private void addshowLink(JMenu linkMenu, String label, final String url)
{
JMenuItem item = new JMenuItem(label);
- item.setToolTipText(MessageManager.formatMessage(
- "label.open_url_param", new Object[] { url }));
+ item.setToolTipText(MessageManager.formatMessage("label.open_url_param",
+ new Object[]
+ { url }));
item.addActionListener(new ActionListener()
{
@Override
final GroupUrlLink urlgenerator, final Object[] urlstub)
{
JMenuItem item = new JMenuItem(label);
- item.setToolTipText(MessageManager.formatMessage(
- "label.open_url_seqs_param",
- new Object[] { urlgenerator.getUrl_prefix(),
+ item.setToolTipText(MessageManager
+ .formatMessage("label.open_url_seqs_param", new Object[]
+ { urlgenerator.getUrl_prefix(),
urlgenerator.getNumberInvolved(urlstub) }));
// TODO: put in info about what is being sent.
item.addActionListener(new ActionListener()
}
});
sequenceMenu.setText(MessageManager.getString("label.sequence"));
- sequenceName.setText(MessageManager
- .getString("label.edit_name_description"));
+ sequenceName.setText(
+ MessageManager.getString("label.edit_name_description"));
sequenceName.addActionListener(new ActionListener()
{
@Override
sequenceName_actionPerformed();
}
});
- chooseAnnotations.setText(MessageManager
- .getString("action.choose_annotations"));
+ chooseAnnotations
+ .setText(MessageManager.getString("action.choose_annotations"));
chooseAnnotations.addActionListener(new ActionListener()
{
@Override
chooseAnnotations_actionPerformed(e);
}
});
- sequenceDetails.setText(MessageManager
- .getString("label.sequence_details"));
+ sequenceDetails
+ .setText(MessageManager.getString("label.sequence_details"));
sequenceDetails.addActionListener(new ActionListener()
{
@Override
sequenceDetails_actionPerformed();
}
});
- sequenceSelDetails.setText(MessageManager
- .getString("label.sequence_details"));
+ sequenceSelDetails
+ .setText(MessageManager.getString("label.sequence_details"));
sequenceSelDetails.addActionListener(new ActionListener()
{
@Override
unGroupMenuItem_actionPerformed();
}
});
- createGroupMenuItem.setText(MessageManager
- .getString("action.create_group"));
+ createGroupMenuItem
+ .setText(MessageManager.getString("action.create_group"));
createGroupMenuItem.addActionListener(new ActionListener()
{
@Override
showColourText_actionPerformed();
}
});
- displayNonconserved.setText(MessageManager
- .getString("label.show_non_conserved"));
+ displayNonconserved
+ .setText(MessageManager.getString("label.show_non_conserved"));
displayNonconserved.setState(true);
displayNonconserved.addActionListener(new ActionListener()
{
changeCase(e);
}
});
- outputMenu.setText(MessageManager.getString("label.out_to_textbox")
- + "...");
- seqShowAnnotationsMenu.setText(MessageManager
- .getString("label.show_annotations"));
- seqHideAnnotationsMenu.setText(MessageManager
- .getString("label.hide_annotations"));
- groupShowAnnotationsMenu.setText(MessageManager
- .getString("label.show_annotations"));
- groupHideAnnotationsMenu.setText(MessageManager
- .getString("label.hide_annotations"));
- sequenceFeature.setText(MessageManager
- .getString("label.create_sequence_feature"));
+ outputMenu.setText(
+ MessageManager.getString("label.out_to_textbox") + "...");
+ seqShowAnnotationsMenu
+ .setText(MessageManager.getString("label.show_annotations"));
+ seqHideAnnotationsMenu
+ .setText(MessageManager.getString("label.hide_annotations"));
+ groupShowAnnotationsMenu
+ .setText(MessageManager.getString("label.show_annotations"));
+ groupHideAnnotationsMenu
+ .setText(MessageManager.getString("label.hide_annotations"));
+ sequenceFeature.setText(
+ MessageManager.getString("label.create_sequence_feature"));
sequenceFeature.addActionListener(new ActionListener()
{
@Override
}
});
jMenu1.setText(MessageManager.getString("label.group"));
- pdbStructureDialog.setText(MessageManager
- .getString("label.show_pdbstruct_dialog"));
+ pdbStructureDialog.setText(
+ MessageManager.getString("label.show_pdbstruct_dialog"));
pdbStructureDialog.addActionListener(new ActionListener()
{
@Override
}
});
- rnaStructureMenu.setText(MessageManager
- .getString("label.view_rna_structure"));
+ rnaStructureMenu
+ .setText(MessageManager.getString("label.view_rna_structure"));
// colStructureMenu.setText("Colour By Structure");
- editSequence.setText(MessageManager.getString("label.edit_sequence")
- + "...");
+ editSequence.setText(
+ MessageManager.getString("label.edit_sequence") + "...");
editSequence.addActionListener(new ActionListener()
{
@Override
editSequence_actionPerformed(actionEvent);
}
});
- makeReferenceSeq.setText(MessageManager
- .getString("label.mark_as_representative"));
+ makeReferenceSeq.setText(
+ MessageManager.getString("label.mark_as_representative"));
makeReferenceSeq.addActionListener(new ActionListener()
{
}
});
- hideInsertions.setText(MessageManager
- .getString("label.hide_insertions"));
+ hideInsertions
+ .setText(MessageManager.getString("label.hide_insertions"));
hideInsertions.addActionListener(new ActionListener()
{
jMenu1.add(outline);
jMenu1.add(displayNonconserved);
}
-
+
/**
* Constructs the entries for the colour menu
*/
}
});
- abovePIDColour.setText(MessageManager
- .getString("label.above_identity_threshold"));
+ abovePIDColour.setText(
+ MessageManager.getString("label.above_identity_threshold"));
abovePIDColour.addActionListener(new ActionListener()
{
@Override
}
});
- modifyPID.setText(MessageManager
- .getString("label.modify_identity_threshold"));
+ modifyPID.setText(
+ MessageManager.getString("label.modify_identity_threshold"));
modifyPID.addActionListener(new ActionListener()
{
@Override
}
});
- conservationMenuItem.setText(MessageManager
- .getString("action.by_conservation"));
+ conservationMenuItem
+ .setText(MessageManager.getString("action.by_conservation"));
conservationMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- conservationMenuItem_actionPerformed(conservationMenuItem
- .isSelected());
+ conservationMenuItem_actionPerformed(
+ conservationMenuItem.isSelected());
}
});
// int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
// .getName());
// sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
- SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
- .getName());
+ SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
SliderPanel.showPIDSlider();
}
}
SortedMap<String, String> tipEntries = new TreeMap<String, String>();
final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
AlignmentI al = this.ap.av.getAlignment();
- AlignmentUtils.findAddableReferenceAnnotations(forSequences,
- tipEntries, candidates, al);
+ AlignmentUtils.findAddableReferenceAnnotations(forSequences, tipEntries,
+ candidates, al);
if (!candidates.isEmpty())
{
StringBuilder tooltip = new StringBuilder(64);
if (ap.av.getSelectionGroup() != null)
{
// mark just the columns in the selection group to be hidden
- inserts.set(ap.av.getSelectionGroup().getStartRes(), ap.av
- .getSelectionGroup().getEndRes() + 1);
+ inserts.set(ap.av.getSelectionGroup().getStartRes(),
+ ap.av.getSelectionGroup().getEndRes() + 1);
// and clear that part of the mask
mask.andNot(inserts);
StringBuilder contents = new StringBuilder(128);
for (SequenceI seq : sequences)
{
- contents.append("<p><h2>"
- + MessageManager
- .formatMessage(
- "label.create_sequence_details_report_annotation_for",
- new Object[] { seq.getDisplayId(true) })
- + "</h2></p><p>");
- new SequenceAnnotationReport(null)
- .createSequenceAnnotationReport(
- contents,
- seq,
- true,
- true,
- (ap.getSeqPanel().seqCanvas.fr != null) ? ap
- .getSeqPanel().seqCanvas.fr.getMinMax()
- : null);
+ contents.append("<p><h2>" + MessageManager.formatMessage(
+ "label.create_sequence_details_report_annotation_for",
+ new Object[]
+ { seq.getDisplayId(true) }) + "</h2></p><p>");
+ new SequenceAnnotationReport(null).createSequenceAnnotationReport(
+ contents, seq, true, true,
+ (ap.getSeqPanel().seqCanvas.fr != null)
+ ? ap.getSeqPanel().seqCanvas.fr.getMinMax()
+ : null);
contents.append("</p>");
}
cap.setText("<html>" + contents.toString() + "</html>");
- Desktop.addInternalFrame(cap, MessageManager.formatMessage(
- "label.sequence_details_for",
- (sequences.length == 1 ? new Object[] { sequences[0]
- .getDisplayId(true) } : new Object[] { MessageManager
- .getString("label.selection") })), 500, 400);
+ Desktop.addInternalFrame(cap,
+ MessageManager.formatMessage("label.sequence_details_for",
+ (sequences.length == 1 ? new Object[]
+ { sequences[0].getDisplayId(true) }
+ : new Object[]
+ { MessageManager
+ .getString("label.selection") })),
+ 500, 400);
}
sg.getStartRes(), sg.getEndRes() + 1));
int threshold = SliderPanel.setPIDSliderSource(ap,
- sg.getGroupColourScheme(), getGroup()
- .getName());
+ sg.getGroupColourScheme(), getGroup().getName());
sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
if (selected)
{
// JBPNote: Conservation name shouldn't be i18n translated
- Conservation c = new Conservation("Group", sg.getSequences(ap.av
- .getHiddenRepSequences()), sg.getStartRes(),
- sg.getEndRes() + 1);
+ Conservation c = new Conservation("Group",
+ sg.getSequences(ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1);
c.calculate();
c.verdict(false, ap.av.getConsPercGaps());
SequenceGroup sg = getGroup();
EditNameDialog dialog = new EditNameDialog(sg.getName(),
- sg.getDescription(), " "
- + MessageManager.getString("label.group_name") + " ",
+ sg.getDescription(),
+ " " + MessageManager.getString("label.group_name") + " ",
MessageManager.getString("label.group_description") + " ",
MessageManager.getString("label.edit_group_name_description"),
ap.alignFrame);
" " + MessageManager.getString("label.sequence_name")
+ " ",
MessageManager.getString("label.sequence_description") + " ",
- MessageManager
- .getString("label.edit_sequence_name_description"),
+ MessageManager.getString(
+ "label.edit_sequence_name_description"),
ap.alignFrame);
if (!dialog.accept)
{
if (dialog.getName().indexOf(" ") > -1)
{
- JvOptionPane
- .showMessageDialog(
- ap,
- MessageManager
- .getString("label.spaces_converted_to_backslashes"),
- MessageManager
- .getString("label.no_spaces_allowed_sequence_name"),
- JvOptionPane.WARNING_MESSAGE);
+ JvOptionPane.showMessageDialog(ap,
+ MessageManager
+ .getString("label.spaces_converted_to_backslashes"),
+ MessageManager
+ .getString("label.no_spaces_allowed_sequence_name"),
+ JvOptionPane.WARNING_MESSAGE);
}
sequence.setName(dialog.getName().replace(' ', '_'));
sequence.setDescription(dialog.getDescription());
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
- .getSequences());
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
}
ap.alignFrame.addHistoryItem(caseCommand);
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
- .getSequences());
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
}
}
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(null);
- Desktop.addInternalFrame(cap, MessageManager.formatMessage(
- "label.alignment_output_command",
- new Object[] { e.getActionCommand() }), 600, 500);
+ Desktop.addInternalFrame(cap, MessageManager
+ .formatMessage("label.alignment_output_command", new Object[]
+ { e.getActionCommand() }), 600, 500);
String[] omitHidden = null;
// or we simply trust the user wants
// wysiwig behaviour
- FileFormatI fileFormat = FileFormats.getInstance().forName(e.getActionCommand());
- cap.setText(new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
+ FileFormatI fileFormat = FileFormats.getInstance()
+ .forName(e.getActionCommand());
+ cap.setText(
+ new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
}
public void sequenceFeature_actionPerformed()
if (start <= end)
{
seqs.add(sg.getSequenceAt(i).getDatasetSequence());
- features.add(new SequenceFeature(null, null, null, start, end, null));
+ features.add(
+ new SequenceFeature(null, null, null, start, end, null));
}
}
*/
if (!seqs.isEmpty())
{
- if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(
- seqs, features, true, ap))
+ if (ap.getSeqPanel().seqCanvas.getFeatureRenderer()
+ .amendFeatures(seqs, features, true, ap))
{
ap.alignFrame.setShowSeqFeatures(true);
ap.highlightSearchResults(null);
EditNameDialog dialog = new EditNameDialog(
sequence.getSequenceAsString(sg.getStartRes(),
- sg.getEndRes() + 1), null,
- MessageManager.getString("label.edit_sequence"), null,
+ sg.getEndRes() + 1),
+ null, MessageManager.getString("label.edit_sequence"), null,
MessageManager.getString("label.edit_sequence"),
ap.alignFrame);
{
EditCommand editCommand = new EditCommand(
MessageManager.getString("label.edit_sequences"),
- Action.REPLACE, dialog.getName().replace(' ',
- ap.av.getGapCharacter()),
+ Action.REPLACE,
+ dialog.getName().replace(' ', ap.av.getGapCharacter()),
sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
ap.alignFrame.addHistoryItem(editCommand);
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
- .getSequences());
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
}
}
}
showUnconserved
.setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
- showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
- false));
- showGroupConservation.setSelected(Cache.getDefault(
- "SHOW_GROUP_CONSERVATION", false));
- showConsensHistogram.setSelected(Cache.getDefault(
- "SHOW_CONSENSUS_HISTOGRAM", true));
- showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
- false));
- showNpTooltip.setSelected(Cache
- .getDefault("SHOW_NPFEATS_TOOLTIP", true));
- showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
- true));
+ showGroupConsensus
+ .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
+ showGroupConservation.setSelected(
+ Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
+ showConsensHistogram.setSelected(
+ Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
+ showConsensLogo
+ .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
+ showNpTooltip
+ .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
+ showDbRefTooltip
+ .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
String[] fonts = java.awt.GraphicsEnvironment
.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
- fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
- + ""));
+ fontStyleCB.setSelectedItem(
+ Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
- scaleProteinToCdna.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA,
- false));
+ scaleProteinToCdna
+ .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
protColour.setSelectedItem(newProp != null ? newProp : oldProp);
newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
- minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
- Color.orange));
- maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
- Color.red));
+ minColour.setBackground(
+ Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
+ maxColour.setBackground(
+ Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
/*
* Set Structure tab defaults.
addSecondaryStructure.setEnabled(structSelected);
addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
addTempFactor.setEnabled(structSelected);
- structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
- ViewerType.JMOL.name()));
+ structViewer.setSelectedItem(
+ Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
chimeraPath.addActionListener(new ActionListener()
{
SortOrder.DESCENDING));
sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
SortOrder.DESCENDING));
- sortKeys.add(new RowSorter.SortKey(m.getNameColumn(),
- SortOrder.ASCENDING));
+ sortKeys.add(
+ new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
sorter.setSortKeys(sortKeys);
sorter.sort();
-
+
// set up filtering
ActionListener onReset;
onReset = new ActionListener()
@Override
public void changedUpdate(DocumentEvent e)
{
- sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag
- + filterTB.getText()));
+ sorter.setRowFilter(RowFilter
+ .regexFilter(caseInsensitiveFlag + filterTB.getText()));
}
@Override
public void removeUpdate(DocumentEvent e)
{
- sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag
- + filterTB.getText()));
+ sorter.setRowFilter(RowFilter
+ .regexFilter(caseInsensitiveFlag + filterTB.getText()));
}
@Override
public void insertUpdate(DocumentEvent e)
{
- sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag
- + filterTB.getText()));
+ sorter.setRowFilter(RowFilter
+ .regexFilter(caseInsensitiveFlag + filterTB.getText()));
}
});
// set up list selection functionality
- linkUrlTable.getSelectionModel().addListSelectionListener(
- new UrlListSelectionHandler());
+ linkUrlTable.getSelectionModel()
+ .addListSelectionListener(new UrlListSelectionHandler());
// set up radio buttons
int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
.getPrimaryColumn();
String onClickName = linkUrlTable.getColumnName(onClickCol);
- linkUrlTable.getColumn(onClickName).setCellRenderer(
- new RadioButtonRenderer());
+ linkUrlTable.getColumn(onClickName)
+ .setCellRenderer(new RadioButtonRenderer());
linkUrlTable.getColumn(onClickName)
.setCellEditor(new RadioButtonEditor());
if (linkUrlTable.getModel().getColumnClass(column)
.equals(Boolean.class))
{
- TableColumn tableColumn = linkUrlTable.getColumnModel().getColumn(
- column);
+ TableColumn tableColumn = linkUrlTable.getColumnModel()
+ .getColumn(column);
int preferredWidth = tableColumn.getMinWidth();
TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
- embbedBioJSON.setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON",
- true));
+ embbedBioJSON
+ .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
/*
* Set Editing tab defaults
*/
- autoCalculateConsCheck.setSelected(Cache.getDefault(
- "AUTO_CALC_CONSENSUS", true));
+ autoCalculateConsCheck
+ .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
Cache.applicationProperties.setProperty("SHOW_IDENTITY",
Boolean.toString(identity.isSelected()));
- Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
- .getSelectedItem().toString());
+ Cache.applicationProperties.setProperty("GAP_SYMBOL",
+ gapSymbolCB.getSelectedItem().toString());
- Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
- .getSelectedItem().toString());
- Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
- .getSelectedItem().toString());
- Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
- .getSelectedItem().toString());
+ Cache.applicationProperties.setProperty("FONT_NAME",
+ fontNameCB.getSelectedItem().toString());
+ Cache.applicationProperties.setProperty("FONT_STYLE",
+ fontStyleCB.getSelectedItem().toString());
+ Cache.applicationProperties.setProperty("FONT_SIZE",
+ fontSizeCB.getSelectedItem().toString());
Cache.applicationProperties.setProperty("ID_ITALICS",
Boolean.toString(idItalics.isSelected()));
Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
Boolean.toString(startupCheckbox.isSelected()));
- Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
- .getSelectedItem().toString());
+ Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
+ sortby.getSelectedItem().toString());
// convert description of sort order to enum name for save
SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
}
final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
- Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean
- .valueOf(showAutocalcFirst).toString());
+ Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
+ Boolean.valueOf(showAutocalcFirst).toString());
/*
* Save Colours settings
*/
- Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour
- .getSelectedItem().toString());
- Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour
- .getSelectedItem().toString());
+ Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
+ protColour.getSelectedItem().toString());
+ Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
+ nucColour.getSelectedItem().toString());
Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
minColour.getBackground());
Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
Boolean.toString(useRnaView.isSelected()));
Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
Boolean.toString(structFromPdb.isSelected()));
- Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
- .getSelectedItem().toString());
+ Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
+ structViewer.getSelectedItem().toString());
Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
Boolean.toString(siftsMapping.isSelected()));
public void startupFileTextfield_mouseClicked()
{
String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
- JalviewFileChooser chooser = JalviewFileChooser.forRead(
- Cache.getProperty("LAST_DIRECTORY"), fileFormat);
+ JalviewFileChooser chooser = JalviewFileChooser
+ .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager
- .getString("label.select_startup_file"));
+ chooser.setDialogTitle(
+ MessageManager.getString("label.select_startup_file"));
int value = chooser.showOpenDialog(this);
Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
format.getName());
}
- startupFileTextfield.setText(chooser.getSelectedFile()
- .getAbsolutePath());
+ startupFileTextfield
+ .setText(chooser.getSelectedFile().getAbsolutePath());
}
}
{
if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
MessageManager.getString("label.new_sequence_url_link"),
- JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
+ JvOptionPane.OK_CANCEL_OPTION, -1,
+ null) == JvOptionPane.OK_OPTION)
{
if (link.checkValid())
{
if (((UrlLinkTableModel) linkUrlTable.getModel())
.isUniqueName(link.getName()))
{
- ((UrlLinkTableModel) linkUrlTable.getModel()).insertRow(
- link.getName(), link.getURL());
+ ((UrlLinkTableModel) linkUrlTable.getModel())
+ .insertRow(link.getName(), link.getURL());
valid = true;
}
else
{
if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
MessageManager.getString("label.edit_sequence_url_link"),
- JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
+ JvOptionPane.OK_CANCEL_OPTION, -1,
+ null) == JvOptionPane.OK_OPTION)
{
if (link.checkValid())
{
((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
}
-
@Override
public void defaultBrowser_mouseClicked(MouseEvent e)
{
JFileChooser chooser = new JFileChooser(".");
- chooser.setDialogTitle(MessageManager
- .getString("label.select_default_browser"));
+ chooser.setDialogTitle(
+ MessageManager.getString("label.select_default_browser"));
int value = chooser.showOpenDialog(this);
}
} catch (NumberFormatException x)
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
- .getString("warn.user_defined_width_requirements"),
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager
+ .getString("warn.user_defined_width_requirements"),
MessageManager.getString("label.invalid_id_column_width"),
JvOptionPane.WARNING_MESSAGE);
userIdWidth.setText("");
if (!found)
{
String[] options = { "OK", "Help" };
- int showHelp = JvOptionPane.showInternalOptionDialog(
- Desktop.desktop,
+ int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
JvSwingUtils.wrapTooltip(true,
MessageManager.getString("label.chimera_missing")),
"", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
return name.hashCode() + code.hashCode();
}
}
-
+
private class UrlListSelectionHandler implements ListSelectionListener
{
editLink.setEnabled(false);
}
}
-}
+ }
}
final JPanel progressPanel = progressBars.get(longId);
if (progressPanel == null)
{
- System.err
- .println("call setProgressBar before registering the progress bar's handler.");
+ System.err.println(
+ "call setProgressBar before registering the progress bar's handler.");
return;
}
public void actionPerformed(ActionEvent e)
{
handler.cancelActivity(id);
- us.setProgressBar(MessageManager.formatMessage(
- "label.cancelled_params",
- new Object[] { ((JLabel) progressPanel.getComponent(0))
- .getText() }), id);
+ us.setProgressBar(MessageManager
+ .formatMessage("label.cancelled_params", new Object[]
+ { ((JLabel) progressPanel.getComponent(0)).getText() }),
+ id);
}
});
progressPanel.add(cancel, BorderLayout.EAST);
}
try
{
- int reply = JvOptionPane.showConfirmDialog(
- Desktop.desktop, // component,
+ int reply = JvOptionPane.showConfirmDialog(Desktop.desktop, // component,
dialogText, dialogTitle,
(allowCancel) ? JvOptionPane.YES_NO_CANCEL_OPTION
: JvOptionPane.YES_NO_OPTION,
{
jalview.bin.Cache.log.warn(
"Unexpected exception when prompting user for yes/no setting for property "
- + property, e);
+ + property,
+ e);
}
}
}
frame = new JInternalFrame();
frame.setContentPane(this);
- Desktop.addInternalFrame(frame, MessageManager
- .getString("label.redundancy_threshold_selection"), 400, 100,
- false);
+ Desktop.addInternalFrame(frame,
+ MessageManager
+ .getString("label.redundancy_threshold_selection"),
+ 400, 100, false);
frame.addInternalFrameListener(new InternalFrameAdapter()
{
@Override
progress.setVisible(false);
progress = null;
- label.setText(MessageManager
- .getString("label.enter_redundancy_threshold"));
+ label.setText(
+ MessageManager.getString("label.enter_redundancy_threshold"));
slider.setVisible(true);
applyButton.setEnabled(true);
valueField.setVisible(true);
ap.alignFrame.addHistoryItem(cut);
PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
- .getSequences());
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
}
}
{
command.undoCommand(af.getViewAlignments());
ap.av.getHistoryList().remove(command);
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
- .getSequences());
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
af.updateEditMenuBar();
}
.newInstance());
} catch (Throwable x)
{
- System.err
- .println("Unexpected exception when instantiating rest input type.");
+ System.err.println(
+ "Unexpected exception when instantiating rest input type.");
x.printStackTrace();
}
return null;
{
okcancel.add(frame.cancel);
okcancel.add(frame.ok);
- frame.initDialogFrame(dpane, true, true, "Edit parameter for service "
- + currentservice.getName(), 600, 800);
+ frame.initDialogFrame(dpane, true, true,
+ "Edit parameter for service " + currentservice.getName(), 600,
+ 800);
initTypeLists();
reply = JvOptionPane.CANCEL_OPTION;
newType.token = tok.getText().trim();
try
{
- newType.configureFromArgumentI(opanps.get(
- newType.getURLtokenPrefix()).getCurrentSettings());
+ newType.configureFromArgumentI(opanps
+ .get(newType.getURLtokenPrefix()).getCurrentSettings());
current = newType;
updated = true;
} catch (InvalidArgumentException ex)
{
- System.err
- .println("IMPLEMENTATION ERROR: Invalid argument for type : "
+ System.err.println(
+ "IMPLEMENTATION ERROR: Invalid argument for type : "
+ typeList.getSelectedValue() + "\n");
ex.printStackTrace();
}
try
{
JPanel inopts = new JPanel(new MigLayout());
- ArrayList<JPanel> opts = new ArrayList<JPanel>(), prms = new ArrayList<JPanel>();
+ ArrayList<JPanel> opts = new ArrayList<JPanel>(),
+ prms = new ArrayList<JPanel>();
jtype = (InputType) (type.getConstructor().newInstance());
typeclass.put(jtype.getURLtokenPrefix(), type);
// and populate parameters from this type
types.add(jtype.getURLtokenPrefix());
} catch (Throwable x)
{
- System.err
- .println("Unexpected exception when instantiating rest input type.");
+ System.err.println(
+ "Unexpected exception when instantiating rest input type.");
x.printStackTrace();
}
}
protected void iprmsAdd_actionPerformed(ActionEvent e)
{
RestInputParamEditDialog dialog = new RestInputParamEditDialog(this,
- currentservice, "param"
- + (1 + currentservice.getInputParams().size()));
+ currentservice,
+ "param" + (1 + currentservice.getInputParams().size()));
if (dialog.wasUpdated())
{
currentservice.getInputParams().put(dialog.current.token,
MessageManager.getString("label.select_return_type"));
for (final JvDataType type : JvDataType.values())
{
- popup.add(new JMenuItem(type.name())).addActionListener(
- new ActionListener()
+ popup.add(new JMenuItem(type.name()))
+ .addActionListener(new ActionListener()
{
@Override
currentservice.addResultDatatype(JvDataType.ANNOTATION);
}
initGuiWith(currentservice);
- rdata.setSelectedIndex(p == -1 ? currentservice.getResultDataTypes()
- .size() - 1 : p + 1);
+ rdata.setSelectedIndex(
+ p == -1 ? currentservice.getResultDataTypes().size() - 1
+ : p + 1);
}
@Override
StringBuffer warnings = new StringBuffer();
for (String its : _iparam)
{
- Matcher mtch = Pattern.compile("(\\S+)\\s(\\S+):\\[(.+)]").matcher(
- its);
+ Matcher mtch = Pattern.compile("(\\S+)\\s(\\S+):\\[(.+)]")
+ .matcher(its);
if (mtch.find())
{
- if (!RestServiceDescription.parseTypeString(mtch.group(2) + ":"
- + mtch.group(3), mtch.group(1), mtch.group(2),
- mtch.group(3), inputTypes, warnings))
+ if (!RestServiceDescription.parseTypeString(
+ mtch.group(2) + ":" + mtch.group(3), mtch.group(1),
+ mtch.group(2), mtch.group(3), inputTypes, warnings))
{
- System.err
- .println("IMPLEMENTATION PROBLEM: Cannot parse RestService input parameter string '"
+ System.err.println(
+ "IMPLEMENTATION PROBLEM: Cannot parse RestService input parameter string '"
+ its + "'" + "\n" + warnings);
}
}
}
- char gc = gapChar.getSelectedItem() == null ? ' ' : ((String) gapChar
- .getSelectedItem()).charAt(0);
+ char gc = gapChar.getSelectedItem() == null ? ' '
+ : ((String) gapChar.getSelectedItem()).charAt(0);
RestServiceDescription newService = new RestServiceDescription(
- (String) action.getSelectedItem(), descr.getText().trim(), name
- .getText().trim(), url.getText().trim(), urlsuff
- .getText().trim(), inputTypes, hSeparable.isSelected(),
+ (String) action.getSelectedItem(), descr.getText().trim(),
+ name.getText().trim(), url.getText().trim(),
+ urlsuff.getText().trim(), inputTypes, hSeparable.isSelected(),
vSeparable.isSelected(), gc);
if (newService.isValid())
} catch (Throwable x)
{
- System.err
- .println("IMPLEMENTATION PROBLEM: Cannot parse RestService output parameter string '"
+ System.err.println(
+ "IMPLEMENTATION PROBLEM: Cannot parse RestService output parameter string '"
+ its + "'" + "\n" + warnings);
}
}
}
else
{
- System.err
- .println("IMPLEMENTATION PROBLEM: Restservice generated from GUI is invalid\n"
+ System.err.println(
+ "IMPLEMENTATION PROBLEM: Restservice generated from GUI is invalid\n"
+ warnings);
}
}
else
{
- parseRes.setText(MessageManager
- .formatMessage(
- "label.parsing_failed_syntax_errors_shown_below_param",
- new String[] { rsd.getInvalidMessage() }));
+ parseRes.setText(MessageManager.formatMessage(
+ "label.parsing_failed_syntax_errors_shown_below_param",
+ new String[]
+ { rsd.getInvalidMessage() }));
parseWarnings.setVisible(true);
}
} catch (Throwable e)
{
e.printStackTrace();
- parseRes.setText(MessageManager
- .formatMessage(
- "label.parsing_failed_unrecoverable_exception_thrown_param",
- new String[] { e.toString() }));
+ parseRes.setText(MessageManager.formatMessage(
+ "label.parsing_failed_unrecoverable_exception_thrown_param",
+ new String[]
+ { e.toString() }));
parseWarnings.setVisible(true);
}
}
final Thread runner = Thread.currentThread();
JFrame df = new JFrame();
df.getContentPane().setLayout(new BorderLayout());
- df.getContentPane().add(
- (nulserv = !nulserv) ? new RestServiceEditorPane(
- jalview.ws.rest.RestClient
- .makeShmmrRestClient()
- .getRestDescription())
- : new RestServiceEditorPane(),
- BorderLayout.CENTER);
+ df.getContentPane().add((nulserv = !nulserv)
+ ? new RestServiceEditorPane(jalview.ws.rest.RestClient
+ .makeShmmrRestClient().getRestDescription())
+ : new RestServiceEditorPane(), BorderLayout.CENTER);
df.setBounds(100, 100, 600, 400);
df.addComponentListener(new ComponentListener()
{
}
};
- JPanel pane = new JPanel(new BorderLayout()), okcancel = new JPanel(
- new FlowLayout());
+ JPanel pane = new JPanel(new BorderLayout()),
+ okcancel = new JPanel(new FlowLayout());
pane.add(this, BorderLayout.CENTER);
okcancel.add(jvd.ok);
okcancel.add(jvd.cancel);
if (points == null)
{
g.setFont(new Font("Verdana", Font.PLAIN, 18));
- g.drawString(MessageManager.getString("label.calculating_pca")
- + "....", 20, getHeight() / 2);
+ g.drawString(
+ MessageManager.getString("label.calculating_pca") + "....",
+ 20, getHeight() / 2);
}
else
{
for (int i = 0; i < 3; i++)
{
- g.drawLine(getWidth() / 2, getHeight() / 2, (int) ((axes[i][0]
- * scale * max[0]) + (getWidth() / 2)), (int) ((axes[i][1]
- * scale * max[1]) + (getHeight() / 2)));
+ g.drawLine(getWidth() / 2, getHeight() / 2,
+ (int) ((axes[i][0] * scale * max[0]) + (getWidth() / 2)),
+ (int) ((axes[i][1] * scale * max[1]) + (getHeight() / 2)));
}
}
{
aps[a].av.setSelectionGroup(new SequenceGroup());
aps[a].av.getSelectionGroup().addOrRemove(found, true);
- aps[a].av.getSelectionGroup().setEndRes(
- aps[a].av.getAlignment().getWidth() - 1);
+ aps[a].av.getSelectionGroup()
+ .setEndRes(aps[a].av.getAlignment().getWidth() - 1);
}
}
PaintRefresher.Refresh(this, av.getSequenceSetId());
for (int i = 0; i < npoint; i++)
{
SequencePoint sp = (SequencePoint) points.elementAt(i);
- int tmp1 = (int) (((sp.coord[0] - centre[0]) * scale) + ((float) getWidth() / 2.0));
- int tmp2 = (int) (((sp.coord[1] - centre[1]) * scale) + ((float) getHeight() / 2.0));
+ int tmp1 = (int) (((sp.coord[0] - centre[0]) * scale)
+ + ((float) getWidth() / 2.0));
+ int tmp2 = (int) (((sp.coord[1] - centre[1]) * scale)
+ + ((float) getHeight() / 2.0));
if ((tmp1 > x1) && (tmp1 < x2) && (tmp2 > y1) && (tmp2 < y2))
{
bg.add(text);
JOptionPane pane = new JOptionPane(null, JvOptionPane.DEFAULT_OPTION,
- JvOptionPane.DEFAULT_OPTION, null, new Object[] { this });
+ JvOptionPane.DEFAULT_OPTION, null, new Object[]
+ { this });
dialog = pane.createDialog(Desktop.desktop, "SVG Rendering options");
dialog.setVisible(true);
* The panel containing the sequence ruler (when not in wrapped mode), and
* supports a range of mouse operations to select, hide or reveal columns.
*/
-public class ScalePanel extends JPanel implements MouseMotionListener,
- MouseListener, ViewportListenerI
+public class ScalePanel extends JPanel
+ implements MouseMotionListener, MouseListener, ViewportListenerI
{
protected int offy = 4;
public void actionPerformed(ActionEvent e)
{
av.hideColumns(res, res);
- if (av.getSelectionGroup() != null
- && av.getSelectionGroup().getSize() == av.getAlignment()
- .getHeight())
+ if (av.getSelectionGroup() != null && av.getSelectionGroup()
+ .getSize() == av.getAlignment().getHeight())
{
av.setSelectionGroup(null);
}
*/
if (!av.getWrapAlignment())
{
- drawScale(g, av.getRanges().getStartRes(),
- av.getRanges().getEndRes(), getWidth(), getHeight());
+ drawScale(g, av.getRanges().getStartRes(), av.getRanges().getEndRes(),
+ getWidth(), getHeight());
}
}
continue;
}
- gg.fillPolygon(new int[] {
- -1 + res * avCharWidth - avCharHeight / 4,
- -1 + res * avCharWidth + avCharHeight / 4,
- -1 + res * avCharWidth }, new int[] { y, y, y + 2 * yOf }, 3);
+ gg.fillPolygon(
+ new int[]
+ { -1 + res * avCharWidth - avCharHeight / 4,
+ -1 + res * avCharWidth + avCharHeight / 4,
+ -1 + res * avCharWidth },
+ new int[]
+ { y, y, y + 2 * yOf }, 3);
}
}
}
{
g.drawString(mstring, mpos * charWidth, ypos - (charHeight / 2));
}
- g.drawLine((mpos * charWidth) + (charWidth / 2), (ypos + 2)
- - (charHeight / 2), (mpos * charWidth) + (charWidth / 2),
- ypos - 2);
+ g.drawLine((mpos * charWidth) + (charWidth / 2),
+ (ypos + 2) - (charHeight / 2),
+ (mpos * charWidth) + (charWidth / 2), ypos - 2);
}
}
}
{
int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))
- charWidth / 2;
- g.drawString(value + "", x, (ypos + (i * charHeight))
- - (charHeight / 5));
+ g.drawString(value + "", x,
+ (ypos + (i * charHeight)) - (charHeight / 5));
}
}
}
if (value != -1)
{
- g.drawString(String.valueOf(value), 0, (ypos + (i * charHeight))
- - (charHeight / 5));
+ g.drawString(String.valueOf(value), 0,
+ (ypos + (i * charHeight)) - (charHeight / 5));
}
}
}
// img and call later.
super.paintComponent(g);
- if (lcimg != null
- && (fastPaint
- || (getVisibleRect().width != g.getClipBounds().width) || (getVisibleRect().height != g
- .getClipBounds().height)))
+ if (lcimg != null && (fastPaint
+ || (getVisibleRect().width != g.getClipBounds().width)
+ || (getVisibleRect().height != g.getClipBounds().height)))
{
g.drawImage(lcimg, 0, 0, this);
fastPaint = false;
}
gg.fillPolygon(
- new int[] { res * charWidth - charHeight / 4,
+ new int[]
+ { res * charWidth - charHeight / 4,
res * charWidth + charHeight / 4, res * charWidth },
- new int[] { ypos - (charHeight / 2),
- ypos - (charHeight / 2), ypos - (charHeight / 2) + 8 },
+ new int[]
+ { ypos - (charHeight / 2), ypos - (charHeight / 2),
+ ypos - (charHeight / 2) + 8 },
3);
}
annotations = new AnnotationPanel(av);
}
- annotations.renderer.drawComponent(annotations, av, g, -1,
- startRes, endx + 1);
+ annotations.renderer.drawComponent(annotations, av, g, -1, startRes,
+ endx + 1);
g.translate(0, -cHeight - ypos - 3);
}
g.setClip(clip);
* @param offset
* DOCUMENT ME!
*/
- public void drawPanel(Graphics g1, int startRes, int endRes,
- int startSeq, int endSeq, int offset)
+ public void drawPanel(Graphics g1, int startRes, int endRes, int startSeq,
+ int endSeq, int offset)
{
updateViewport();
if (!av.hasHiddenColumns())
if (av.isShowSequenceFeatures())
{
- fr.drawSequence(g, nextSeq, startRes, endRes, offset
- + ((i - startSeq) * charHeight), false);
+ fr.drawSequence(g, nextSeq, startRes, endRes,
+ offset + ((i - startSeq) * charHeight), false);
}
// / Highlight search Results once all sequences have been drawn
for (int r = 0; r < visibleResults.length; r += 2)
{
sr.drawHighlightedText(nextSeq, visibleResults[r],
- visibleResults[r + 1], (visibleResults[r] - startRes)
- * charWidth, offset
- + ((i - startSeq) * charHeight));
+ visibleResults[r + 1],
+ (visibleResults[r] - startRes) * charWidth,
+ offset + ((i - startSeq) * charHeight));
}
}
}
{
sx = (group.getStartRes() - startRes) * charWidth;
sy = offset + ((i - startSeq) * charHeight);
- ex = (((group.getEndRes() + 1) - group.getStartRes()) * charWidth) - 1;
+ ex = (((group.getEndRes() + 1) - group.getStartRes()) * charWidth)
+ - 1;
if (sx + ex < 0 || sx > visWidth)
{
}
if ((sx <= (endRes - startRes) * charWidth)
- && group.getSequences(null).contains(
- av.getAlignment().getSequenceAt(i)))
+ && group.getSequences(null)
+ .contains(av.getAlignment().getSequenceAt(i)))
{
- if ((bottom == -1)
- && !group.getSequences(null).contains(
- av.getAlignment().getSequenceAt(i + 1)))
+ if ((bottom == -1) && !group.getSequences(null)
+ .contains(av.getAlignment().getSequenceAt(i + 1)))
{
bottom = sy + charHeight;
}
if (!inGroup)
{
- if (((top == -1) && (i == 0))
- || !group.getSequences(null).contains(
- av.getAlignment().getSequenceAt(i - 1)))
+ if (((top == -1) && (i == 0)) || !group.getSequences(null)
+ .contains(av.getAlignment().getSequenceAt(i - 1)))
{
top = sy;
}
if (group == av.getSelectionGroup())
{
g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT,
- BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f },
- 0f));
+ BasicStroke.JOIN_ROUND, 3f, new float[]
+ { 5f, 3f }, 0f));
g.setColor(Color.RED);
}
else
* @author $author$
* @version $Revision: 1.130 $
*/
-public class SeqPanel extends JPanel implements MouseListener,
- MouseMotionListener, MouseWheelListener, SequenceListener,
- SelectionListener
+public class SeqPanel extends JPanel
+ implements MouseListener, MouseMotionListener, MouseWheelListener,
+ SequenceListener, SelectionListener
{
/** DOCUMENT ME!! */
y -= hgap;
- seq = Math.min((y % cHeight) / av.getCharHeight(), av.getAlignment()
- .getHeight() - 1);
+ seq = Math.min((y % cHeight) / av.getCharHeight(),
+ av.getAlignment().getHeight() - 1);
}
else
{
- seq = Math.min((y / av.getCharHeight())
- + av.getRanges().getStartSeq(),
- av
- .getAlignment().getHeight() - 1);
+ seq = Math.min(
+ (y / av.getCharHeight()) + av.getRanges().getStartSeq(),
+ av.getAlignment().getHeight() - 1);
}
return seq;
if (editCommand != null && editCommand.getSize() > 0)
{
ap.alignFrame.addHistoryItem(editCommand);
- av.firePropertyChange("alignment", null, av.getAlignment()
- .getSequences());
+ av.firePropertyChange("alignment", null,
+ av.getAlignment().getSequences());
}
} finally
{
HiddenColumns hidden = av.getAlignment().getHiddenColumns();
- if (av.hasHiddenColumns()
- && !hidden.isVisible(seqCanvas.cursorX))
+ if (av.hasHiddenColumns() && !hidden.isVisible(seqCanvas.cursorX))
{
int original = seqCanvas.cursorX - dx;
int maxWidth = av.getAlignment().getWidth();
Point p = lastp;
if (!event.isShiftDown() || p == null)
{
- p = (tooltipText != null && tooltipText.length() > 6) ? new Point(
- event.getX() + wdth, event.getY() - 20) : null;
+ p = (tooltipText != null && tooltipText.length() > 6)
+ ? new Point(event.getX() + wdth, event.getY() - 20)
+ : null;
}
/*
* TODO: try to modify position region is not obcured by tooltip
}
else
{
- residue = "X".equalsIgnoreCase(displayChar) ? "X" : ("*"
- .equals(displayChar) ? "STOP"
- : ResidueProperties.aa2Triplet.get(displayChar));
+ residue = "X".equalsIgnoreCase(displayChar) ? "X"
+ : ("*".equals(displayChar) ? "STOP"
+ : ResidueProperties.aa2Triplet.get(displayChar));
}
text.append(" ").append(nucleotide ? "Nucleotide" : "Residue")
.append(": ").append(residue == null ? displayChar : residue);
int oldWidth = av.getCharWidth();
// Which is bigger, left-right or up-down?
- if (Math.abs(evt.getY() - lastMousePress.getY()) > Math.abs(evt
- .getX() - lastMousePress.getX()))
+ if (Math.abs(evt.getY() - lastMousePress.getY()) > Math
+ .abs(evt.getX() - lastMousePress.getX()))
{
/*
* on drag up or down, decrement or increment font size
}
if (editCommand == null)
{
- editCommand = new EditCommand(MessageManager.formatMessage(
- "label.edit_params", new String[] { label }));
+ editCommand = new EditCommand(MessageManager
+ .formatMessage("label.edit_params", new String[]
+ { label }));
}
}
ap.alignFrame.statusBar.setText(message.toString());
// Are we editing within a selection group?
- if (groupEditing
- || (sg != null && sg.getSequences(av.getHiddenRepSequences())
- .contains(seq)))
+ if (groupEditing || (sg != null
+ && sg.getSequences(av.getHiddenRepSequences()).contains(seq)))
{
fixedColumns = true;
}
else
{
- appendEdit(Action.INSERT_GAP, groupSeqs, startres, startres
- - lastres);
+ appendEdit(Action.INSERT_GAP, groupSeqs, startres,
+ startres - lastres);
}
}
else
}
else
{
- appendEdit(Action.DELETE_GAP, groupSeqs, startres, lastres
- - startres);
+ appendEdit(Action.DELETE_GAP, groupSeqs, startres,
+ lastres - startres);
}
}
* highlight the first feature at the position on the alignment
*/
SearchResultsI highlight = new SearchResults();
- highlight.addResult(sequence, features.get(0).getBegin(), features
- .get(0).getEnd());
+ highlight.addResult(sequence, features.get(0).getBegin(),
+ features.get(0).getEnd());
seqCanvas.highlightSearchResults(highlight);
/*
if (av.getWrapAlignment() && seq > av.getAlignment().getHeight())
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
- .getString("label.cannot_edit_annotations_in_wrapped_view"),
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString(
+ "label.cannot_edit_annotations_in_wrapped_view"),
MessageManager.getString("label.wrapped_view_no_edit"),
JvOptionPane.WARNING_MESSAGE);
return;
stretchGroup.cs.alignmentChanged(stretchGroup,
av.getHiddenRepSequences());
- ResidueShaderI groupColourScheme = stretchGroup.getGroupColourScheme();
+ ResidueShaderI groupColourScheme = stretchGroup
+ .getGroupColourScheme();
String name = stretchGroup.getName();
if (stretchGroup.cs.conservationApplied())
{
running = av.getRanges().scrollUp(true);
}
- if (mouseDragging && (evt.getY() >= getHeight())
- && (av.getAlignment().getHeight() > av.getRanges()
- .getEndSeq()))
+ if (mouseDragging && (evt.getY() >= getHeight()) && (av
+ .getAlignment().getHeight() > av.getRanges().getEndSeq()))
{
running = av.getRanges().scrollUp(false);
}
// handles selection messages...
// TODO: extend config options to allow user to control if selections may be
// shared between viewports.
- boolean iSentTheSelection = (av == source || (source instanceof AlignViewport && ((AlignmentViewport) source)
- .getSequenceSetId().equals(av.getSequenceSetId())));
+ boolean iSentTheSelection = (av == source
+ || (source instanceof AlignViewport
+ && ((AlignmentViewport) source).getSequenceSetId()
+ .equals(av.getSequenceSetId())));
if (iSentTheSelection)
{
repaint = true;
}
- if (copycolsel
- && av.hasHiddenColumns()
+ if (copycolsel && av.hasHiddenColumns()
&& (av.getAlignment().getHiddenColumns() == null))
{
System.err.println("Bad things");
{
if (guiWindow != null)
{
- guiWindow
- .setProgressBar(
- MessageManager
- .getString("status.waiting_sequence_database_fetchers_init"),
- Thread.currentThread().hashCode());
+ guiWindow.setProgressBar(
+ MessageManager.getString(
+ "status.waiting_sequence_database_fetchers_init"),
+ Thread.currentThread().hashCode());
}
// initting happening on another thread - so wait around to see if it
// finishes.
}
if (guiWindow != null)
{
- guiWindow
- .setProgressBar(
- MessageManager
- .getString("status.waiting_sequence_database_fetchers_init"),
- Thread.currentThread().hashCode());
+ guiWindow.setProgressBar(
+ MessageManager.getString(
+ "status.waiting_sequence_database_fetchers_init"),
+ Thread.currentThread().hashCode());
}
}
- if (sfetch == null
- || dasRegistry != Cache.getDasSourceRegistry()
+ if (sfetch == null || dasRegistry != Cache.getDasSourceRegistry()
|| lastDasSourceRegistry != (Cache.getDasSourceRegistry()
- .getDasRegistryURL() + Cache.getDasSourceRegistry()
- .getLocalSourceString()).hashCode())
+ .getDasRegistryURL()
+ + Cache.getDasSourceRegistry().getLocalSourceString())
+ .hashCode())
{
_initingFetcher = true;
initingThread = Thread.currentThread();
*/
if (guiWindow != null)
{
- guiWindow.setProgressBar(MessageManager
- .getString("status.init_sequence_database_fetchers"),
+ guiWindow.setProgressBar(
+ MessageManager.getString(
+ "status.init_sequence_database_fetchers"),
Thread.currentThread().hashCode());
}
dasRegistry = Cache.getDasSourceRegistry();
{
guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
}
- lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry
- .getLocalSourceString()).hashCode();
+ lastDasSourceRegistry = (dasRegistry.getDasRegistryURL()
+ + dasRegistry.getLocalSourceString()).hashCode();
sfetch = sf;
_initingFetcher = false;
initingThread = null;
@Override
public void run()
{
- JvOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- MessageManager
- .getString("warn.couldnt_create_sequence_fetcher_client"),
- MessageManager
- .getString("label.couldnt_create_sequence_fetcher"),
- JvOptionPane.ERROR_MESSAGE);
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString(
+ "warn.couldnt_create_sequence_fetcher_client"),
+ MessageManager.getString(
+ "label.couldnt_create_sequence_fetcher"),
+ JvOptionPane.ERROR_MESSAGE);
}
});
if (sourcep.getTier() == 0)
{
database.selection = Arrays
- .asList(new DbSourceProxy[] { sourcep });
+ .asList(new DbSourceProxy[]
+ { sourcep });
break;
}
}
if (database.selection == null || database.selection.size() == 0)
{
- System.err.println("Ignoring fetch parameter db='" + selectedDb
- + "'");
+ System.err.println(
+ "Ignoring fetch parameter db='" + selectedDb + "'");
return false;
}
textArea.setText(queryString);
private String getFrameTitle()
{
- return ((alignFrame == null) ? MessageManager
- .getString("label.new_sequence_fetcher") : MessageManager
- .getString("label.additional_sequence_fetcher"));
+ return ((alignFrame == null)
+ ? MessageManager.getString("label.new_sequence_fetcher")
+ : MessageManager
+ .getString("label.additional_sequence_fetcher"));
}
private void jbInit() throws Exception
replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
replacePunctuation
.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
- replacePunctuation.setText(MessageManager
- .getString("label.replace_commas_semicolons"));
+ replacePunctuation.setText(
+ MessageManager.getString("label.replace_commas_semicolons"));
ok.setText(MessageManager.getString("action.ok"));
ok.addActionListener(new ActionListener()
{
+ database.getSelectedSources().size() + " others)"
: ""));
String eq = database.getExampleQueries();
- dbeg.setText(MessageManager.formatMessage(
- "label.example_query_param", new String[] { eq }));
+ dbeg.setText(MessageManager.formatMessage("label.example_query_param",
+ new String[]
+ { eq }));
boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
for (DbSourceProxy dbs : database.getSelectedSources())
{
if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
{
empty = new com.stevesoft.pat.Regex(
- // replace commas and spaces with a semicolon
+ // replace commas and spaces with a semicolon
"(\\s|[,; ])+", ";");
}
else
}
textArea.setText(empty.replaceAll(textArea.getText()));
// see if there's anthing to search with
- if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea
- .getText()))
+ if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]")
+ .search(textArea.getText()))
{
error += "Please enter a (semi-colon separated list of) database id(s)";
}
Iterator<DbSourceProxy> proxies = database.getSelectedSources()
.iterator();
String[] qries;
- List<String> nextFetch = Arrays.asList(qries = textArea.getText()
- .split(";"));
+ List<String> nextFetch = Arrays
+ .asList(qries = textArea.getText().split(";"));
Iterator<String> en = Arrays.asList(new String[0]).iterator();
int nqueries = qries.length;
try
{
// update status
- guiWindow
- .setProgressBar(MessageManager.formatMessage(
- "status.fetching_sequence_queries_from",
- new String[] {
- Integer.valueOf(nqueries).toString(),
- proxy.getDbName() }), Thread.currentThread()
- .hashCode());
+ guiWindow.setProgressBar(MessageManager.formatMessage(
+ "status.fetching_sequence_queries_from", new String[]
+ { Integer.valueOf(nqueries).toString(),
+ proxy.getDbName() }),
+ Thread.currentThread().hashCode());
if (proxy.getMaximumQueryCount() == 1)
{
/*
}
} catch (Exception e)
{
- showErrorMessage("Error retrieving " + textArea.getText()
- + " from " + database.getSelectedItem());
+ showErrorMessage("Error retrieving " + textArea.getText() + " from "
+ + database.getSelectedItem());
// error
// +="Couldn't retrieve sequences from "+database.getSelectedItem();
System.err.println("Retrieval failed for source ='"
} catch (OutOfMemoryError e)
{
showErrorMessage("Out of Memory when retrieving "
- + textArea.getText()
- + " from "
- + database.getSelectedItem()
+ + textArea.getText() + " from " + database.getSelectedItem()
+ "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
e.printStackTrace();
} catch (Error e)
while (aresult.size() > 0)
{
presult.add(aresult.remove(0));
- presultTitle.add(aresultq.remove(0) + " "
- + getDefaultRetrievalTitle());
+ presultTitle.add(
+ aresultq.remove(0) + " " + getDefaultRetrievalTitle());
}
}
else
presultTitle.add(titl);
}
}
- guiWindow.setProgressBar(MessageManager
- .getString("status.finshed_querying"), Thread.currentThread()
- .hashCode());
+ guiWindow.setProgressBar(
+ MessageManager.getString("status.finshed_querying"),
+ Thread.currentThread().hashCode());
}
- guiWindow.setProgressBar(
- (presult.size() > 0) ? MessageManager
- .getString("status.parsing_results") : MessageManager
- .getString("status.processing"), Thread.currentThread()
- .hashCode());
+ guiWindow
+ .setProgressBar(
+ (presult.size() > 0)
+ ? MessageManager
+ .getString("status.parsing_results")
+ : MessageManager.getString("status.processing"),
+ Thread.currentThread().hashCode());
// process results
while (presult.size() > 0)
{
{
StringBuffer sb = new StringBuffer();
sb.append("Didn't retrieve the following "
- + (nextFetch.size() == 1 ? "query" : nextFetch.size()
- + " queries") + ": \n");
+ + (nextFetch.size() == 1 ? "query"
+ : nextFetch.size() + " queries")
+ + ": \n");
int l = sb.length(), lr = 0;
for (String s : nextFetch)
{
*/
void fetchMultipleAccessions(DbSourceProxy proxy,
Iterator<String> accessions, List<String> aresultq,
- List<AlignmentI> aresult, List<String> nextFetch)
- throws Exception
+ List<AlignmentI> aresult, List<String> nextFetch) throws Exception
{
StringBuilder multiacc = new StringBuilder();
List<String> tosend = new ArrayList<String>();
indres = proxy.getSequenceRecords(accession);
} catch (OutOfMemoryError oome)
{
- new OOMWarning("fetching " + accession + " from "
- + proxy.getDbName(), oome, this);
+ new OOMWarning(
+ "fetching " + accession + " from " + proxy.getDbName(),
+ oome, this);
}
if (indres != null)
{
}
} catch (Exception e)
{
- Cache.log.info(
- "Error retrieving " + accession + " from "
- + proxy.getDbName(), e);
+ Cache.log.info("Error retrieving " + accession + " from "
+ + proxy.getDbName(), e);
}
return success;
}
// If EPS graphics, stringWidth will be a double, not an int
double dwidth = fm.getStringBounds("M", g).getWidth();
- monospacedFont = (dwidth == fm.getStringBounds("|", g).getWidth() && av
- .getCharWidth() == dwidth);
+ monospacedFont = (dwidth == fm.getStringBounds("|", g).getWidth()
+ && av.getCharWidth() == dwidth);
this.renderGaps = renderGaps;
}
{
if (shader.getColourScheme() != null)
{
- resBoxColour = shader.findColour(seq.getCharAt(i),
- i, seq);
+ resBoxColour = shader.findColour(seq.getCharAt(i), i, seq);
}
else if (forOverview && !Comparison.isGap(seq.getCharAt(i)))
{
int length = seq.getLength();
int curStart = -1;
- int curWidth = av.getCharWidth(), avWidth = av.getCharWidth(), avHeight = av
- .getCharHeight();
+ int curWidth = av.getCharWidth(), avWidth = av.getCharWidth(),
+ avHeight = av.getCharHeight();
Color tempColour = null;
else
{
char gap = av.getGapCharacter();
- graphics.drawString(seq.getSequenceAsString(start, end + 1)
- .replace(gap, ' '), 0, y1);
+ graphics.drawString(
+ seq.getSequenceAsString(start, end + 1).replace(gap, ' '),
+ 0, y1);
}
}
else
boolean srep = av.isDisplayReferenceSeq();
boolean getboxColour = false;
boolean isarep = av.getAlignment().getSeqrep() == seq;
- boolean isgrep = currentSequenceGroup != null ? currentSequenceGroup
- .getSeqrep() == seq : false;
+ boolean isgrep = currentSequenceGroup != null
+ ? currentSequenceGroup.getSeqrep() == seq
+ : false;
char sr_c;
for (int i = start; i <= end; i++)
{
if (currentSequenceGroup.thresholdTextColour > 0)
{
if (resBoxColour.getRed() + resBoxColour.getBlue()
- + resBoxColour.getGreen() < currentSequenceGroup.thresholdTextColour)
+ + resBoxColour
+ .getGreen() < currentSequenceGroup.thresholdTextColour)
{
graphics.setColor(currentSequenceGroup.textColour2);
}
// currentSequenceGroup.getConsensus()
char conschar = (usesrep) ? (currentGroup == null
|| position < currentGroup.getStartRes()
- || position > currentGroup.getEndRes() ? av.getAlignment()
- .getSeqrep().getCharAt(position)
- : (currentGroup.getSeqrep() != null ? currentGroup.getSeqrep()
- .getCharAt(position) : av.getAlignment().getSeqrep()
- .getCharAt(position)))
+ || position > currentGroup.getEndRes()
+ ? av.getAlignment().getSeqrep().getCharAt(position)
+ : (currentGroup.getSeqrep() != null
+ ? currentGroup.getSeqrep().getCharAt(position)
+ : av.getAlignment().getSeqrep()
+ .getCharAt(position)))
: (currentGroup != null && currentGroup.getConsensus() != null
&& position >= currentGroup.getStartRes()
- && position <= currentGroup.getEndRes() && currentGroup
- .getConsensus().annotations.length > position) ? currentGroup
- .getConsensus().annotations[position].displayCharacter
- .charAt(0)
- : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
- .charAt(0);
+ && position <= currentGroup.getEndRes()
+ && currentGroup
+ .getConsensus().annotations.length > position)
+ ? currentGroup
+ .getConsensus().annotations[position].displayCharacter
+ .charAt(0)
+ : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
+ .charAt(0);
if (!jalview.util.Comparison.isGap(conschar)
- && (sequenceChar == conschar || sequenceChar + CHAR_TO_UPPER == conschar))
+ && (sequenceChar == conschar
+ || sequenceChar + CHAR_TO_UPPER == conschar))
{
sequenceChar = conservedChar;
}
* @param height
* DOCUMENT ME!
*/
- public void drawHighlightedText(SequenceI seq, int start, int end,
- int x1, int y1)
+ public void drawHighlightedText(SequenceI seq, int start, int end, int x1,
+ int y1)
{
int pady = av.getCharHeight() / 5;
int charOffset = 0;
if (forConservation)
{
- label.setText(MessageManager
- .getString("label.enter_value_increase_conservation_visibility"));
+ label.setText(MessageManager.getString(
+ "label.enter_value_increase_conservation_visibility"));
slider.setMinimum(0);
slider.setMaximum(100);
}
else
{
- label.setText(MessageManager
- .getString("label.enter_percentage_identity_above_which_colour_residues"));
+ label.setText(MessageManager.getString(
+ "label.enter_percentage_identity_above_which_colour_residues"));
slider.setMinimum(0);
slider.setMaximum(100);
}
else
{
sliderPanel = (SliderPanel) conservationSlider.getContentPane();
- sliderPanel.valueField.setText(String.valueOf(rs.getConservationInc()));
+ sliderPanel.valueField
+ .setText(String.valueOf(rs.getConservationInc()));
sliderPanel.cs = rs;
sliderPanel.ap = ap;
sliderPanel.slider.setValue(rs.getConservationInc());
}
conservationSlider.setTitle(MessageManager.formatMessage(
- "label.conservation_colour_increment",
- new String[] { source == null ? BACKGROUND : source }));
+ "label.conservation_colour_increment", new String[]
+ { source == null ? BACKGROUND : source }));
List<SequenceGroup> groups = ap.av.getAlignment().getGroups();
if (groups != null && !groups.isEmpty())
{
Desktop.addInternalFrame(conservationSlider,
conservationSlider.getTitle(), 420, 90, false);
- conservationSlider
- .addInternalFrameListener(new InternalFrameAdapter()
- {
- @Override
- public void internalFrameClosed(InternalFrameEvent e)
- {
- conservationSlider = null;
- }
- });
+ conservationSlider.addInternalFrameListener(new InternalFrameAdapter()
+ {
+ @Override
+ public void internalFrameClosed(InternalFrameEvent e)
+ {
+ conservationSlider = null;
+ }
+ });
conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
}
}
*
* @return
*/
- public static int setPIDSliderSource(AlignmentPanel ap,
- ResidueShaderI rs, String source)
+ public static int setPIDSliderSource(AlignmentPanel ap, ResidueShaderI rs,
+ String source)
{
int threshold = rs.getThreshold();
}
PIDSlider.setTitle(MessageManager.formatMessage(
- "label.percentage_identity_threshold",
- new String[] { source == null ? BACKGROUND : source }));
+ "label.percentage_identity_threshold", new String[]
+ { source == null ? BACKGROUND : source }));
if (ap.av.getAlignment().getGroups() != null)
{
static int getValue(JInternalFrame slider)
{
- return slider == null ? 0 : ((SliderPanel) slider.getContentPane())
- .getValue();
+ return slider == null ? 0
+ : ((SliderPanel) slider.getContentPane()).getValue();
}
public static int getPIDValue()
* @author $author$
* @version $Revision$
*/
-public class SplashScreen extends JPanel implements Runnable,
- HyperlinkListener
+public class SplashScreen extends JPanel
+ implements Runnable, HyperlinkListener
{
boolean visible = true;
try
{
java.net.URL url = getClass().getResource("/images/Jalview_Logo.png");
- java.net.URL urllogo = getClass().getResource(
- "/images/Jalview_Logo_small.png");
+ java.net.URL urllogo = getClass()
+ .getResource("/images/Jalview_Logo_small.png");
if (url != null)
{
image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
- Image logo = java.awt.Toolkit.getDefaultToolkit().createImage(
- urllogo);
+ Image logo = java.awt.Toolkit.getDefaultToolkit()
+ .createImage(urllogo);
MediaTracker mt = new MediaTracker(this);
mt.addImage(image, 0);
mt.addImage(logo, 1);
{
// allow about 65 pixels for Desktop decorators on Windows
- int newHeight = Math.min(height, Desktop.instance.getHeight()
- - DESKTOP_DECORATORS_HEIGHT);
+ int newHeight = Math.min(height,
+ Desktop.instance.getHeight() - DESKTOP_DECORATORS_HEIGHT);
if (newHeight != height)
{
int oldDividerLocation = getDividerLocation();
/*
* Ctrl-W / Cmd-W - close view or window
*/
- KeyStroke key_cmdW = KeyStroke.getKeyStroke(KeyEvent.VK_W, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ KeyStroke key_cmdW = KeyStroke.getKeyStroke(KeyEvent.VK_W,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
action = new AbstractAction()
{
@Override
/*
* Ctrl-T / Cmd-T open new view
*/
- KeyStroke key_cmdT = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ KeyStroke key_cmdT = KeyStroke.getKeyStroke(KeyEvent.VK_T,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
AbstractAction action = new AbstractAction()
{
@Override
Component c = getFrameAtMouse();
if (c != null && c instanceof AlignFrame)
{
- for (ActionListener a : ((AlignFrame) c).getAccelerators()
- .get(ks).getActionListeners())
+ for (ActionListener a : ((AlignFrame) c).getAccelerators().get(ks)
+ .getActionListeners())
{
a.actionPerformed(null);
}
*/
public List<AlignFrame> getAlignFrames()
{
- return Arrays.asList(new AlignFrame[] { (AlignFrame) getTopFrame(),
- (AlignFrame) getBottomFrame() });
+ return Arrays
+ .asList(new AlignFrame[]
+ { (AlignFrame) getTopFrame(), (AlignFrame) getBottomFrame() });
}
/**
/*
* Ctrl-F / Cmd-F open Finder dialog, 'focused' on the right alignment
*/
- KeyStroke key_cmdF = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ KeyStroke key_cmdF = KeyStroke.getKeyStroke(KeyEvent.VK_F,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
AbstractAction action = new AbstractAction()
{
@Override
*
*/
@SuppressWarnings("serial")
-public class StructureChooser extends GStructureChooser implements
- IProgressIndicator
+public class StructureChooser extends GStructureChooser
+ implements IProgressIndicator
{
private static int MAX_QLENGTH = 7820;
.getString("status.loading_cached_pdb_entries"), startTime);
loadLocalCachedPDBEntries();
updateProgressIndicator(null, startTime);
- updateProgressIndicator(MessageManager
- .getString("status.searching_for_pdb_structures"),
- startTime);
+ updateProgressIndicator(MessageManager.getString(
+ "status.searching_for_pdb_structures"), startTime);
fetchStructuresMetaData();
// revise filter options if no results were found
populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists);
if (discoveredStructuresSet != null
&& !discoveredStructuresSet.isEmpty())
{
- getResultTable().setModel(
- FTSRestResponse.getTableModel(lastPdbRequest,
- discoveredStructuresSet));
+ getResultTable().setModel(FTSRestResponse
+ .getTableModel(lastPdbRequest, discoveredStructuresSet));
noOfStructuresFound = discoveredStructuresSet.size();
mainFrame.setTitle(MessageManager.formatMessage(
"label.structure_chooser_no_of_structures",
{
if (isValidSeqName(entry.getId()))
{
- queryBuilder.append("pdb_id:")
- .append(entry.getId().toLowerCase()).append(" OR ");
+ queryBuilder.append("pdb_id:").append(entry.getId().toLowerCase())
+ .append(" OR ");
isPDBRefsFound = true;
}
}
Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<FTSData>();
reorderedStructuresSet.addAll(filteredResponse);
reorderedStructuresSet.addAll(discoveredStructuresSet);
- getResultTable().setModel(
- FTSRestResponse.getTableModel(lastPdbRequest,
- reorderedStructuresSet));
+ getResultTable().setModel(FTSRestResponse
+ .getTableModel(lastPdbRequest, reorderedStructuresSet));
FTSRestResponse.configureTableColumn(getResultTable(),
wantedFields, tempUserPrefs);
{
errorMsg.append(error).append("\n");
}
- JvOptionPane.showMessageDialog(
- null,
- errorMsg.toString(),
+ JvOptionPane.showMessageDialog(null, errorMsg.toString(),
MessageManager.getString("label.pdb_web-service_error"),
JvOptionPane.ERROR_MESSAGE);
}
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle(MessageManager.formatMessage(
- "label.select_pdb_file_for",
- selectedSequence.getDisplayId(false)));
+ chooser.setDialogTitle(
+ MessageManager.formatMessage("label.select_pdb_file_for",
+ selectedSequence.getDisplayId(false)));
chooser.setToolTipText(MessageManager.formatMessage(
"label.load_pdb_file_associate_with_sequence",
selectedSequence.getDisplayId(false)));
cmb_filterOption.addItem(new FilterOption("Most Polymer Residues",
"number_of_polymer_residues", VIEWS_FILTER, true));
}
- cmb_filterOption.addItem(new FilterOption("Enter PDB Id", "-",
- VIEWS_ENTER_ID, false));
- cmb_filterOption.addItem(new FilterOption("From File", "-",
- VIEWS_FROM_FILE, false));
+ cmb_filterOption.addItem(
+ new FilterOption("Enter PDB Id", "-", VIEWS_ENTER_ID, false));
+ cmb_filterOption.addItem(
+ new FilterOption("From File", "-", VIEWS_FROM_FILE, false));
if (cachedPDBExists)
{
lbl_pdbManualFetchStatus.setToolTipText("");
if (txt_search.getText().length() > 0)
{
- lbl_pdbManualFetchStatus
- .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
- .formatMessage("info.no_pdb_entry_found_for",
- txt_search.getText())));
+ lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager.formatMessage("info.no_pdb_entry_found_for",
+ txt_search.getText())));
}
if (errorWarning.length() > 0)
{
lbl_pdbManualFetchStatus.setIcon(warningImage);
- lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(
- true, errorWarning.toString()));
+ lbl_pdbManualFetchStatus.setToolTipText(
+ JvSwingUtils.wrapTooltip(true, errorWarning.toString()));
}
- if (selectedSequences.length == 1
- || !assSeqOpt.getName().equalsIgnoreCase(
- "-Select Associated Seq-"))
+ if (selectedSequences.length == 1 || !assSeqOpt.getName()
+ .equalsIgnoreCase("-Select Associated Seq-"))
{
txt_search.setEnabled(true);
if (isValidPBDEntry)
AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
.getCmb_assSeq().getSelectedItem();
lbl_fromFileStatus.setIcon(errorImage);
- if (selectedSequences.length == 1
- || (assSeqOpt != null && !assSeqOpt.getName().equalsIgnoreCase(
- "-Select Associated Seq-")))
+ if (selectedSequences.length == 1 || (assSeqOpt != null && !assSeqOpt
+ .getName().equalsIgnoreCase("-Select Associated Seq-")))
{
btn_pdbFromFile.setEnabled(true);
if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
List<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
for (int row : selectedRows)
{
- String pdbIdStr = getResultTable().getValueAt(row,
- pdbIdColIndex).toString();
+ String pdbIdStr = getResultTable()
+ .getValueAt(row, pdbIdColIndex).toString();
SequenceI selectedSeq = (SequenceI) getResultTable()
.getValueAt(row, refSeqColIndex);
selectedSeqsToView.add(selectedSeq);
PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
pdbIdColIndex);
pdbEntriesToView[count++] = pdbEntry;
- SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt(
- row, refSeqColIndex);
+ SequenceI selectedSeq = (SequenceI) tbl_local_pdb
+ .getValueAt(row, refSeqColIndex);
selectedSeqsToView.add(selectedSeq);
}
SequenceI[] selectedSeqs = selectedSeqsToView
PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
launchStructureViewer(ssm, pdbEntriesToView, ap,
- new SequenceI[] { selectedSequence });
- }
- else if (currentView == VIEWS_FROM_FILE)
- {
- SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
- .getCmb_assSeq().getSelectedItem()).getSequence();
- if (userSelectedSeq != null)
- {
- selectedSequence = userSelectedSeq;
- }
- PDBEntry fileEntry = new AssociatePdbFileWithSeq()
- .associatePdbWithSeq(selectedPdbFileName,
- DataSourceType.FILE,
- selectedSequence, true, Desktop.instance);
+ new SequenceI[]
+ { selectedSequence });
+ }
+ else if (currentView == VIEWS_FROM_FILE)
+ {
+ SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
+ .getCmb_assSeq().getSelectedItem()).getSequence();
+ if (userSelectedSeq != null)
+ {
+ selectedSequence = userSelectedSeq;
+ }
+ PDBEntry fileEntry = new AssociatePdbFileWithSeq()
+ .associatePdbWithSeq(selectedPdbFileName,
+ DataSourceType.FILE, selectedSequence, true,
+ Desktop.instance);
launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
- new SequenceI[] { selectedSequence });
+ new SequenceI[]
+ { selectedSequence });
}
closeAction(preferredHeight);
}
}
SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]);
ssm.setProgressBar(null);
- ssm.setProgressBar(MessageManager
- .getString("status.fetching_3d_structures_for_selected_entries"));
+ ssm.setProgressBar(MessageManager.getString(
+ "status.fetching_3d_structures_for_selected_entries"));
sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel);
}
else
*/
@Override
public void populateCmbAssociateSeqOptions(
- JComboBox<AssociateSeqOptions> cmb_assSeq, JLabel lbl_associateSeq)
+ JComboBox<AssociateSeqOptions> cmb_assSeq,
+ JLabel lbl_associateSeq)
{
cmb_assSeq.removeAllItems();
- cmb_assSeq.addItem(new AssociateSeqOptions("-Select Associated Seq-",
- null));
+ cmb_assSeq.addItem(
+ new AssociateSeqOptions("-Select Associated Seq-", null));
lbl_associateSeq.setVisible(false);
if (selectedSequences.length > 1)
{
public void run()
{
fetchStructuresMetaData();
- filterResultSet(((FilterOption) cmb_filterOption
- .getSelectedItem()).getValue());
+ filterResultSet(
+ ((FilterOption) cmb_filterOption.getSelectedItem())
+ .getValue());
}
});
refreshThread.start();
public class PDBEntryTableModel extends AbstractTableModel
{
- String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type", "File" };
+ String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type",
+ "File" };
private List<CachedPDB> pdbEntries;
value = entry.getPdbEntry();
break;
case 2:
- value = entry.getPdbEntry().getChainCode() == null ? "_" : entry
- .getPdbEntry().getChainCode();
+ value = entry.getPdbEntry().getChainCode() == null ? "_"
+ : entry.getPdbEntry().getChainCode();
break;
case 3:
value = entry.getPdbEntry().getType();
Cache.setProperty(Preferences.STRUCTURE_DISPLAY, type.name());
}
- public StructureViewer(StructureSelectionManager structureSelectionManager)
+ public StructureViewer(
+ StructureSelectionManager structureSelectionManager)
{
ssm = structureSelectionManager;
}
}
}
}
- return viewStructures(pdbs[0],
- seqs.toArray(new SequenceI[seqs.size()]), ap);
+ return viewStructures(pdbs[0], seqs.toArray(new SequenceI[seqs.size()]),
+ ap);
}
public JalviewStructureDisplayI viewStructures(PDBEntry pdb,
JalviewStructureDisplayI sview = null;
if (viewerType.equals(ViewerType.JMOL))
{
- sview = new AppJmol(ap, pdbsForFile, ap.av.collateForPDB(pdbsForFile));
+ sview = new AppJmol(ap, pdbsForFile,
+ ap.av.collateForPDB(pdbsForFile));
}
else if (viewerType.equals(ViewerType.CHIMERA))
{
* @param vid
* @return
*/
- public JalviewStructureDisplayI createView(ViewerType type,
- String[] pdbf, String[] id, SequenceI[][] sq,
- AlignmentPanel alignPanel, StructureViewerModel viewerData,
- String fileloc, Rectangle rect, String vid)
+ public JalviewStructureDisplayI createView(ViewerType type, String[] pdbf,
+ String[] id, SequenceI[][] sq, AlignmentPanel alignPanel,
+ StructureViewerModel viewerData, String fileloc, Rectangle rect,
+ String vid)
{
final boolean useinViewerSuperpos = viewerData.isAlignWithPanel();
final boolean usetoColourbyseq = viewerData.isColourWithAlignPanel();
useinViewerSuperpos, viewerColouring, fileloc, rect, vid);
break;
case CHIMERA:
- Cache.log.error("Unsupported structure viewer type "
- + type.toString());
+ Cache.log.error(
+ "Unsupported structure viewer type " + type.toString());
break;
default:
Cache.log.error("Unknown structure viewer type " + type.toString());
{
super();
}
+
/**
*
* @param ap2
}
// otherwise, start adding the structure.
getBinding().addSequenceAndChain(new PDBEntry[] { pdbentry },
- new SequenceI[][] { seqs }, new String[][] { chains });
+ new SequenceI[][]
+ { seqs }, new String[][] { chains });
addingStructures = true;
_started = false;
alignAddedStructures = align;
{
int option = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
MessageManager.formatMessage("label.add_pdbentry_to_view",
- new Object[] { pdbId, view.getTitle() }),
+ new Object[]
+ { pdbId, view.getTitle() }),
MessageManager
.getString("label.align_to_existing_structure_view"),
JvOptionPane.YES_NO_CANCEL_OPTION);
*/
viewer.useAlignmentPanelForColourbyseq(apanel);
viewer.buildActionMenu();
- apanel.getStructureSelectionManager().sequenceColoursChanged(
- apanel);
+ apanel.getStructureSelectionManager()
+ .sequenceColoursChanged(apanel);
break;
}
}
*/
int option = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
MessageManager.formatMessage(
- "label.pdb_entry_is_already_displayed",
- new Object[] { pdbId }), MessageManager
- .formatMessage(
- "label.map_sequences_to_visible_window",
- new Object[] { pdbId }),
+ "label.pdb_entry_is_already_displayed", new Object[]
+ { pdbId }),
+ MessageManager.formatMessage(
+ "label.map_sequences_to_visible_window", new Object[]
+ { pdbId }),
JvOptionPane.YES_NO_CANCEL_OPTION);
if (option == JvOptionPane.CANCEL_OPTION)
{
public void changeColour_actionPerformed(String colourSchemeName)
{
AlignmentI al = getAlignmentPanel().av.getAlignment();
- ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(
- colourSchemeName, al, null);
+ ColourSchemeI cs = ColourSchemes.getInstance()
+ .getColourScheme(colourSchemeName, al, null);
getBinding().setJalviewColourScheme(cs);
}
}
@Override
- public void setJalviewColourScheme(ColourSchemeI cs) {
+ public void setJalviewColourScheme(ColourSchemeI cs)
+ {
getBinding().setJalviewColourScheme(cs);
}
* the operation.
*/
@Override
- protected String alignStructs_actionPerformed(
- ActionEvent actionEvent)
+ protected String alignStructs_actionPerformed(ActionEvent actionEvent)
{
return alignStructs_withAllAlignPanels();
}
{
return null;
}
-
+
if (_alignwith.size() == 0)
{
_alignwith.add(getAlignmentPanel());
}
-
+
String reply = null;
try
{
HiddenColumns[] alc = new HiddenColumns[_alignwith.size()];
int[] alm = new int[_alignwith.size()];
int a = 0;
-
+
for (AlignmentPanel ap : _alignwith)
{
als[a] = ap.av.getAlignment();
reply = getBinding().superposeStructures(als, alm, alc);
if (reply != null)
{
- String text = MessageManager.formatMessage(
- "error.superposition_failed", reply);
+ String text = MessageManager
+ .formatMessage("error.superposition_failed", reply);
statusBar.setText(text);
}
} catch (Exception e)
getBinding().setBackgroundColour(col);
}
}
+
@Override
public void viewerColour_actionPerformed(ActionEvent actionEvent)
{
getBinding().setColourBySequence(false);
}
}
+
@Override
public void chainColour_actionPerformed(ActionEvent actionEvent)
{
chainColour.setSelected(true);
getBinding().colourByChain();
}
+
@Override
public void chargeColour_actionPerformed(ActionEvent actionEvent)
{
chargeColour.setSelected(true);
getBinding().colourByCharge();
}
+
@Override
public void seqColour_actionPerformed(ActionEvent actionEvent)
{
}
}
}
+
@Override
public void pdbFile_actionPerformed(ActionEvent actionEvent)
{
JalviewFileChooser chooser = new JalviewFileChooser(
Cache.getProperty("LAST_DIRECTORY"));
-
+
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
chooser.setToolTipText(MessageManager.getString("action.save"));
-
+
int value = chooser.showSaveDialog(this);
-
+
if (value == JalviewFileChooser.APPROVE_OPTION)
{
BufferedReader in = null;
in = new BufferedReader(
new FileReader(getBinding().getStructureFiles()[0]));
File outFile = chooser.getSelectedFile();
-
+
PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
String data;
while ((data = in.readLine()) != null)
}
}
}
+
@Override
public void viewMapping_actionPerformed(ActionEvent actionEvent)
{
return;
}
setChainMenuItems(binding.getChainNames());
-
+
this.setTitle(binding.getViewerTitle(getViewerName(), true));
/*
* @param sequenceGroup
* the SequenceGroup context (only for group pop-menu option)
*/
- public void chooseColour(AlignmentPanel alignPanel, SequenceGroup sequenceGroup)
+ public void chooseColour(AlignmentPanel alignPanel,
+ SequenceGroup sequenceGroup)
{
this.ap = alignPanel;
this.sg = sequenceGroup;
JPanel panel = new JPanel();
bigpanel.add(panel, BorderLayout.CENTER);
bigpanel.add(
- new JLabel(
- "<html>"
- + MessageManager
- .getString("label.select_dark_light_set_threshold")
- + "</html>"), BorderLayout.NORTH);
+ new JLabel("<html>"
+ + MessageManager.getString(
+ "label.select_dark_light_set_threshold")
+ + "</html>"),
+ BorderLayout.NORTH);
panel.add(col1);
panel.add(slider);
panel.add(col2);
}
});
- int reply = JvOptionPane
- .showInternalOptionDialog(
- alignPanel,
- bigpanel,
- MessageManager
- .getString("label.adjunst_foreground_text_colour_threshold"),
- JvOptionPane.OK_CANCEL_OPTION,
- JvOptionPane.QUESTION_MESSAGE, null, null, null);
+ int reply = JvOptionPane.showInternalOptionDialog(alignPanel, bigpanel,
+ MessageManager.getString(
+ "label.adjunst_foreground_text_colour_threshold"),
+ JvOptionPane.OK_CANCEL_OPTION, JvOptionPane.QUESTION_MESSAGE,
+ null, null, null);
if (reply == JvOptionPane.CANCEL_OPTION)
{
g.drawString(nodeLabel, xstart + 2, ypos - 2);
}
- String name = (markPlaceholders && node.isPlaceholder()) ? (PLACEHOLDER + node
- .getName()) : node.getName();
+ String name = (markPlaceholders && node.isPlaceholder())
+ ? (PLACEHOLDER + node.getName())
+ : node.getName();
int charWidth = fm.stringWidth(name) + 3;
int charHeight = font.getSize();
g.fillRect(xend - 2, ypos - 2, 4, 4);
}
- int ystart = (node.left() == null ? 0 : (int) (((SequenceNode) node
- .left()).ycount * chunk)) + offy;
- int yend = (node.right() == null ? 0 : (int) (((SequenceNode) node
- .right()).ycount * chunk))
+ int ystart = (node.left() == null ? 0
+ : (int) (((SequenceNode) node.left()).ycount * chunk)) + offy;
+ int yend = (node.right() == null ? 0
+ : (int) (((SequenceNode) node.right()).ycount * chunk))
+ offy;
Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);
SequenceNode top = tree.getTopNode();
- double wscale = ((width * .8) - (offx * 2))
- / tree.getMaxHeight();
+ double wscale = ((width * .8) - (offx * 2)) / tree.getMaxHeight();
if (top.count == 0)
{
if (tree == null)
{
- g.drawString(MessageManager.getString("label.calculating_tree")
- + "....", 20, getHeight() / 2);
+ g.drawString(
+ MessageManager.getString("label.calculating_tree") + "....",
+ 20, getHeight() / 2);
}
else
{
repaint();
}
- if (fitToWindow
- || (!fitToWindow && (scrollPane.getHeight() > ((fm
- .getHeight() * nameHash.size()) + offy))))
+ if (fitToWindow || (!fitToWindow && (scrollPane
+ .getHeight() > ((fm.getHeight() * nameHash.size()) + offy))))
{
draw(g, scrollPane.getWidth(), scrollPane.getHeight());
setPreferredSize(null);
g2.setColor(Color.gray);
}
- int x = (int) ((threshold * (getWidth() - labelLength - (2 * offx))) + offx);
+ int x = (int) ((threshold * (getWidth() - labelLength - (2 * offx)))
+ + offx);
g2.drawLine(x, 0, x, getHeight());
}
if (ob instanceof SequenceNode)
{
highlightNode = (SequenceNode) ob;
- this.setToolTipText("<html>"
- + MessageManager.getString("label.highlightnode"));
+ this.setToolTipText(
+ "<html>" + MessageManager.getString("label.highlightnode"));
repaint();
}
}
else
{
- cs = ColourSchemeProperty.getColourScheme(sg,
- ColourSchemeProperty.getColourName(av
- .getGlobalColourScheme()));
+ cs = ColourSchemeProperty.getColourScheme(sg, ColourSchemeProperty
+ .getColourName(av.getGlobalColourScheme()));
}
// cs is null if shading is an annotationColourGradient
// if (cs != null)
for (int a = 0; a < aps.length; a++)
{
if (aps[a].av.getGlobalColourScheme() != null
- && aps[a].av.getResidueShading()
- .conservationApplied())
+ && aps[a].av.getResidueShading().conservationApplied())
{
Conservation c = new Conservation("Group", sg.getSequences(null),
sg.getStartRes(), sg.getEndRes());
}
if (evt.getNewValue() == null)
{
- System.out
- .println("new alignment sequences vector value is null");
+ System.out.println(
+ "new alignment sequences vector value is null");
}
tree.updatePlaceHolders((List<SequenceI>) evt.getNewValue());
void buildAssociatedViewMenu()
{
- AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
- .getSequenceSetId());
+ AlignmentPanel[] aps = PaintRefresher
+ .getAssociatedPanels(av.getSequenceSetId());
if (aps.length == 1 && treeCanvas.ap == aps[0])
{
associateLeavesMenu.setVisible(false);
associateLeavesMenu.setVisible(true);
- if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
+ if ((viewMenu
+ .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
{
viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
}
}
else
{
- ScoreModelI sm = ScoreModels.getInstance().getScoreModel(
- scoreModelName, treeCanvas.ap);
- TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING) ? new NJTree(
- av, sm, similarityParams) : new AverageDistanceTree(av, sm,
- similarityParams);
+ ScoreModelI sm = ScoreModels.getInstance()
+ .getScoreModel(scoreModelName, treeCanvas.ap);
+ TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
+ ? new NJTree(av, sm, similarityParams)
+ : new AverageDistanceTree(av, sm, similarityParams);
tree = new TreeModel(njtree);
showDistances(true);
}
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager
- .getString("label.save_tree_as_newick"));
+ chooser.setDialogTitle(
+ MessageManager.getString("label.save_tree_as_newick"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(null);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
- .getSelectedFile().getParent());
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+ chooser.getSelectedFile().getParent());
try
{
jalview.io.NewickFile fout = new jalview.io.NewickFile(
tree.getTopNode());
- String output = fout.print(tree.hasBootstrap(),
- tree.hasDistances(), tree.hasRootDistance());
+ String output = fout.print(tree.hasBootstrap(), tree.hasDistances(),
+ tree.hasRootDistance());
java.io.PrintWriter out = new java.io.PrintWriter(
new java.io.FileWriter(choice));
out.println(output);
AlignmentView originalData = tree.getOriginalData();
if (originalData == null)
{
- jalview.bin.Cache.log
- .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
+ jalview.bin.Cache.log.info(
+ "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
return;
}
// decide if av alignment is sufficiently different to original data to
// AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
- AlignmentI dataset = (av != null && av.getAlignment() != null) ? av
- .getAlignment().getDataset() : null;
+ AlignmentI dataset = (av != null && av.getAlignment() != null)
+ ? av.getAlignment().getDataset()
+ : null;
if (dataset != null)
{
al.setDataset(dataset);
{
// make a new frame!
AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
// >>>This is a fix for the moment, until a better solution is
// found!!<<<
// msaorder);
Desktop.addInternalFrame(af, MessageManager.formatMessage(
- "label.original_data_for_params",
- new Object[] { this.title }), AlignFrame.DEFAULT_WIDTH,
+ "label.original_data_for_params", new Object[]
+ { this.title }), AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
}
}
if (treeCanvas.applyToAllViews)
{
final ArrayList<CommandI> commands = new ArrayList<CommandI>();
- for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
- .getSequenceSetId()))
+ for (AlignmentPanel ap : PaintRefresher
+ .getAssociatedPanels(av.getSequenceSetId()))
{
commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
}
}
}
});
- for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
- .getSequenceSetId()))
+ for (AlignmentPanel ap : PaintRefresher
+ .getAssociatedPanels(av.getSequenceSetId()))
{
// ensure all the alignFrames refresh their GI after adding an undo item
ap.alignFrame.updateEditMenuBar();
JalviewFileChooser chooser = new JalviewFileChooser(
ImageMaker.EPS_EXTENSION, ImageMaker.EPS_EXTENSION);
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager
- .getString("label.create_eps_from_tree"));
+ chooser.setDialogTitle(
+ MessageManager.getString("label.create_eps_from_tree"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
return;
}
- Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile()
- .getParent());
+ Cache.setProperty("LAST_DIRECTORY",
+ chooser.getSelectedFile().getParent());
- FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
- EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);
+ FileOutputStream out = new FileOutputStream(
+ chooser.getSelectedFile());
+ EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
+ height);
pg.setAccurateTextMode(accurateText);
ImageMaker.PNG_EXTENSION, ImageMaker.PNG_DESCRIPTION);
chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle(MessageManager
- .getString("label.create_png_from_tree"));
+ chooser.setDialogTitle(
+ MessageManager.getString("label.create_png_from_tree"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
return;
}
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
- .getSelectedFile().getParent());
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+ chooser.getSelectedFile().getParent());
- FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
+ FileOutputStream out = new FileOutputStream(
+ chooser.getSelectedFile());
BufferedImage bi = new BufferedImage(width, height,
BufferedImage.TYPE_INT_RGB);
if (sq != null)
{
// search dbrefs, features and annotation
- DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(
- sq.getDBRefs(),
- new String[] { labelClass.toUpperCase() });
+ DBRefEntry[] refs = jalview.util.DBRefUtils
+ .selectRefs(sq.getDBRefs(), new String[]
+ { labelClass.toUpperCase() });
if (refs != null)
{
for (int i = 0; i < refs.length; i++)
* Neighbour Joining Using BLOSUM62
* <p>
* For a tree loaded from file, just uses the file name
+ *
* @return
*/
public String getPanelTitle()
/*
* i18n description of Neighbour Joining or Average Distance method
*/
- String treecalcnm = MessageManager.getString("label.tree_calc_"
- + treeType.toLowerCase());
+ String treecalcnm = MessageManager
+ .getString("label.tree_calc_" + treeType.toLowerCase());
/*
* short score model name (long description can be too long)
* @author Andrew Waterhouse
* @author Mungo Carstairs
*/
-public class UserDefinedColours extends GUserDefinedColours implements
- ChangeListener
+public class UserDefinedColours extends GUserDefinedColours
+ implements ChangeListener
{
- private static final Font VERDANA_BOLD_10 = new Font("Verdana",
- Font.BOLD, 10);
+ private static final Font VERDANA_BOLD_10 = new Font("Verdana", Font.BOLD,
+ 10);
public static final String USER_DEFINED_COLOURS = "USER_DEFINED_COLOURS";
if (oldColourScheme instanceof UserColourScheme)
{
schemeName.setText(oldColourScheme.getSchemeName());
- if (((UserColourScheme) oldColourScheme).getLowerCaseColours() != null)
+ if (((UserColourScheme) oldColourScheme)
+ .getLowerCaseColours() != null)
{
caseSensitive.setSelected(true);
lcaseColour.setEnabled(true);
{
button = lowerCaseButtons.get(i);
button.setBackground(newColour);
- button.setForeground(ColorUtils.brighterThan(button.getBackground()));
+ button.setForeground(
+ ColorUtils.brighterThan(button.getBackground()));
}
}
for (int i = 0; i < selectedButtons.size(); i++)
JButton button = (JButton) buttonPanel.getComponent(b);
if (!selectedButtons.contains(button))
{
- button.setForeground(ColorUtils.brighterThan(button
- .getBackground()));
+ button.setForeground(
+ ColorUtils.brighterThan(button.getBackground()));
selectedButtons.add(button);
}
}
button.setForeground(ColorUtils.darkerThan(button.getBackground()));
}
selectedButtons.clear();
- pressed.setForeground(ColorUtils.brighterThan(pressed.getBackground()));
+ pressed.setForeground(
+ ColorUtils.brighterThan(pressed.getBackground()));
selectedButtons.add(pressed);
}
{
if (selectedButtons.contains(pressed))
{
- pressed.setForeground(ColorUtils.darkerThan(pressed.getBackground()));
+ pressed.setForeground(
+ ColorUtils.darkerThan(pressed.getBackground()));
selectedButtons.remove(pressed);
}
else
{
- pressed.setForeground(ColorUtils.brighterThan(pressed
- .getBackground()));
+ pressed.setForeground(
+ ColorUtils.brighterThan(pressed.getBackground()));
selectedButtons.add(pressed);
}
}
{
if (isNoSelectionMade())
{
- JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
- .getString("label.no_colour_selection_in_scheme"),
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ MessageManager
+ .getString("label.no_colour_selection_in_scheme"),
MessageManager.getString("label.no_colour_selection_warn"),
JvOptionPane.WARNING_MESSAGE);
}
{
if (isNoSelectionMade())
{
- JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
- .getString("label.no_colour_selection_in_scheme"),
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ MessageManager
+ .getString("label.no_colour_selection_in_scheme"),
MessageManager.getString("label.no_colour_selection_warn"),
JvOptionPane.WARNING_MESSAGE);
JalviewFileChooser chooser = new JalviewFileChooser("jc",
"Jalview User Colours");
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager
- .getString("label.load_colour_scheme"));
+ chooser.setDialogTitle(
+ MessageManager.getString("label.load_colour_scheme"));
chooser.setToolTipText(MessageManager.getString("action.load"));
int value = chooser.showOpenDialog(this);
File choice = chooser.getSelectedFile();
Cache.setProperty(LAST_DIRECTORY, choice.getParent());
- UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(choice
- .getAbsolutePath());
+ UserColourScheme ucs = ColourSchemeLoader
+ .loadColourScheme(choice.getAbsolutePath());
Color[] colors = ucs.getColours();
schemeName.setText(ucs.getSchemeName());
* name if overwriting</li>
* <li>Do the standard file chooser thing to write with extension .jc</li>
* <li>If saving changes (possibly not yet applied) to the currently selected
- * colour scheme, then apply the changes, as it is too late to back out now</li>
+ * colour scheme, then apply the changes, as it is too late to back out
+ * now</li>
* <li>Don't apply the changes if the currently selected scheme is different,
* to allow a new scheme to be configured and saved but not applied</li>
* </ul>
String name = schemeName.getText().trim();
if (name.length() < 1)
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
- .getString("label.user_colour_scheme_must_have_name"),
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager
+ .getString("label.user_colour_scheme_must_have_name"),
MessageManager.getString("label.no_name_colour_scheme"),
JvOptionPane.WARNING_MESSAGE);
return false;
{
int reply = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
MessageManager.formatMessage(
- "label.colour_scheme_exists_overwrite", new Object[] {
- name, name }),
+ "label.colour_scheme_exists_overwrite", new Object[]
+ { name, name }),
MessageManager.getString("label.duplicate_scheme_name"),
JvOptionPane.YES_NO_OPTION);
if (reply != JvOptionPane.YES_OPTION)
JalviewFileView fileView = new JalviewFileView();
chooser.setFileView(fileView);
- chooser.setDialogTitle(MessageManager
- .getString("label.save_colour_scheme"));
+ chooser.setDialogTitle(
+ MessageManager.getString("label.save_colour_scheme"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
* update the delimited list of user defined colour files in
* Jalview property USER_DEFINED_COLOURS
*/
- String defaultColours = Cache
- .getDefault(USER_DEFINED_COLOURS, filePath);
+ String defaultColours = Cache.getDefault(USER_DEFINED_COLOURS,
+ filePath);
if (defaultColours.indexOf(filePath) == -1)
{
if (defaultColours.length() > 0)
{
if (url.indexOf("questionnaire.pl") == -1)
{
- jalview.bin.Cache.log
- .error("'"
- + url
- + "' is an Invalid URL for the checkForQuestionnaire() method.\n"
- + "This argument is only for questionnaires derived from jalview's questionnaire.pl cgi interface.");
+ jalview.bin.Cache.log.error("'" + url
+ + "' is an Invalid URL for the checkForQuestionnaire() method.\n"
+ + "This argument is only for questionnaires derived from jalview's questionnaire.pl cgi interface.");
}
else
{
boolean prompt = false;
// see if we have already responsed to this questionnaire or get a new
// qid/rid pair
- BufferedReader br = new BufferedReader(new InputStreamReader(
- qurl.openStream()));
+ BufferedReader br = new BufferedReader(
+ new InputStreamReader(qurl.openStream()));
String qresp;
while ((qresp = br.readLine()) != null)
{
String qurl = url + (url.indexOf('?') > -1 ? "&" : "?")
+ "checkresponse=1";
// query the server with the old qid/id pair
- String qqid = lastq.indexOf(':') > -1 ? lastq.substring(0,
- lastq.indexOf(':')) : null;
+ String qqid = lastq.indexOf(':') > -1
+ ? lastq.substring(0, lastq.indexOf(':'))
+ : null;
if (qqid != null && qqid != "null" && qqid.length() > 0)
{
qurl += "&qid=" + qqid;
{
String qurl = url + (url.indexOf('?') > -1 ? "&" : "?") + "qid="
+ qid + "&rid=" + rid;
- jalview.bin.Cache.log.info("Prompting user for questionnaire at "
- + qurl);
- int reply = JvOptionPane
- .showInternalConfirmDialog(Desktop.desktop, MessageManager
- .getString("label.jalview_new_questionnaire"),
- MessageManager
- .getString("label.jalview_user_survey"),
- JvOptionPane.YES_NO_OPTION,
- JvOptionPane.QUESTION_MESSAGE);
+ jalview.bin.Cache.log
+ .info("Prompting user for questionnaire at " + qurl);
+ int reply = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ MessageManager.getString("label.jalview_new_questionnaire"),
+ MessageManager.getString("label.jalview_user_survey"),
+ JvOptionPane.YES_NO_OPTION, JvOptionPane.QUESTION_MESSAGE);
if (reply == JvOptionPane.YES_OPTION)
{
}
} catch (Exception e)
{
- jalview.bin.Cache.log.warn("When trying to access questionnaire URL "
- + url, e);
+ jalview.bin.Cache.log
+ .warn("When trying to access questionnaire URL " + url, e);
}
}
{
if (sess != null)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_cannot_import_vamsas_doc"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_cannot_import_vamsas_doc"));
}
try
{
}
} catch (InvalidSessionDocumentException e)
{
- JvOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager
- .getString("label.vamsas_doc_couldnt_be_opened_as_new_session"),
- MessageManager
- .getString("label.vamsas_document_import_failed"),
- JvOptionPane.ERROR_MESSAGE);
+ MessageManager.getString(
+ "label.vamsas_doc_couldnt_be_opened_as_new_session"),
+ MessageManager
+ .getString("label.vamsas_document_import_failed"),
+ JvOptionPane.ERROR_MESSAGE);
}
}
} catch (Exception e)
{
- jalview.bin.Cache.log
- .error("Couldn't instantiate vamsas client !", e);
+ jalview.bin.Cache.log.error("Couldn't instantiate vamsas client !",
+ e);
return false;
}
return true;
}
} catch (Error e)
{
- Cache.log
- .warn("Probable SERIOUS VAMSAS client incompatibility - carrying on regardless",
- e);
+ Cache.log.warn(
+ "Probable SERIOUS VAMSAS client incompatibility - carrying on regardless",
+ e);
} catch (Exception e)
{
- Cache.log
- .warn("Probable VAMSAS client incompatibility - carrying on regardless",
- e);
+ Cache.log.warn(
+ "Probable VAMSAS client incompatibility - carrying on regardless",
+ e);
}
}
{
if (!inSession())
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_vamsas_operation_not_init"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_vamsas_operation_not_init"));
}
addDocumentUpdateHandler();
addStoreDocumentHandler();
startSession();
inInitialUpdate = true;
- Cache.log
- .debug("Jalview loading the Vamsas Session for the first time.");
+ Cache.log.debug(
+ "Jalview loading the Vamsas Session for the first time.");
dealWithDocumentUpdate(false); // we don't push an update out to the
inInitialUpdate = false;
// document yet.
}
} catch (Exception e)
{
- Cache.log
- .warn("Exception whilst refreshing jalview windows after a vamsas document update.",
- e);
+ Cache.log.warn(
+ "Exception whilst refreshing jalview windows after a vamsas document update.",
+ e);
}
}
{
if (!inSession())
{
- throw new Error(
- MessageManager
- .getString("error.jalview_no_connected_vamsas_session"));
+ throw new Error(MessageManager
+ .getString("error.jalview_no_connected_vamsas_session"));
}
Cache.log.info("Jalview disconnecting from the Vamsas Session.");
try
}
else
{
- Cache.log
- .warn("JV Client leaving a session that's its not joined yet.");
+ Cache.log.warn(
+ "JV Client leaving a session that's its not joined yet.");
}
joinedSession = false;
vclient = null;
} catch (Exception e)
{
errorsDuringUpdate = true;
- Cache.log.error("Exception synchronizing "
- + af.getTitle()
+ Cache.log.error("Exception synchronizing " + af.getTitle()
+ " "
- + (af.getViewport().viewName == null ? "" : " view "
- + af.getViewport().viewName)
+ + (af.getViewport().viewName == null ? ""
+ : " view " + af.getViewport().viewName)
+ " to document.", e);
stored = false;
}
storedviews += updateVamsasDocument(cdoc);
if (Cache.log.isDebugEnabled())
{
- Cache.log
- .debug("Time taken to update Vamsas Document from jalview\t= "
+ Cache.log.debug(
+ "Time taken to update Vamsas Document from jalview\t= "
+ (System.currentTimeMillis() - time));
time = System.currentTimeMillis();
}
updateJalview(cdoc);
if (Cache.log.isDebugEnabled())
{
- Cache.log
- .debug("Time taken to update Jalview from vamsas document Roots\t= "
+ Cache.log.debug(
+ "Time taken to update Jalview from vamsas document Roots\t= "
+ (System.currentTimeMillis() - time));
time = System.currentTimeMillis();
}
{
if (client.promptUser)
{
- Cache.log
- .debug("Asking user if the vamsas session should be stored.");
- int reply = JvOptionPane
- .showInternalConfirmDialog(
- Desktop.desktop,
- "The current VAMSAS session has unsaved data - do you want to save it ?",
- "VAMSAS Session Shutdown",
- JvOptionPane.YES_NO_OPTION,
- JvOptionPane.QUESTION_MESSAGE);
+ Cache.log.debug(
+ "Asking user if the vamsas session should be stored.");
+ int reply = JvOptionPane.showInternalConfirmDialog(
+ Desktop.desktop,
+ "The current VAMSAS session has unsaved data - do you want to save it ?",
+ "VAMSAS Session Shutdown",
+ JvOptionPane.YES_NO_OPTION,
+ JvOptionPane.QUESTION_MESSAGE);
if (reply == JvOptionPane.YES_OPTION)
{
Cache.log
.debug("Finished attempt at storing document.");
}
- Cache.log
- .debug("finished dealing with REQUESTTOCLOSE event.");
+ Cache.log.debug(
+ "finished dealing with REQUESTTOCLOSE event.");
}
else
{
- Cache.log
- .debug("Ignoring store document request (promptUser==false)");
+ Cache.log.debug(
+ "Ignoring store document request (promptUser==false)");
}
}
});
return;
}
- throw new Error(
- MessageManager
- .getString("error.implementation_error_cannot_recover_vamsas_object_mappings"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_cannot_recover_vamsas_object_mappings"));
}
jv2vobj.clear();
Iterator el = _backup_jv2vobj.entrySet().iterator();
{
jselection.setStartRes(prange[p + l] - 1);
}
- if (jselection.getEndRes() <= maxWidth
- && prange[p + u] == (jselection.getEndRes() + 2))
+ if (jselection.getEndRes() <= maxWidth && prange[p
+ + u] == (jselection.getEndRes() + 2))
{
jselection.setEndRes(prange[p + u] - 1);
}
{
if (vobj2jv == null)
{
- Cache.log
- .warn("Selection listener still active for dead session.");
+ Cache.log.warn(
+ "Selection listener still active for dead session.");
// not in a session.
return;
}
}
SelectionMessage sm = null;
if ((seqsel == null || seqsel.getSize() == 0)
- && (colsel == null || colsel.getSelected() == null || colsel
- .getSelected().size() == 0))
+ && (colsel == null || colsel.getSelected() == null
+ || colsel.getSelected().size() == 0))
{
if (source instanceof AlignViewport)
{
// the empty selection.
sm = new SelectionMessage("jalview",
- new String[] { ((AlignmentViewport) source)
- .getSequenceSetId() }, null, true);
+ new String[]
+ { ((AlignmentViewport) source)
+ .getSequenceSetId() },
+ null, true);
}
else
{
append = append || _selectedviews.size() > 1;
toggleview = new JCheckBoxMenuItem(
MessageManager.getString("label.select_many_views"), append);
- toggleview.setToolTipText(MessageManager
- .getString("label.toggle_enabled_views"));
+ toggleview.setToolTipText(
+ MessageManager.getString("label.toggle_enabled_views"));
toggleview.addItemListener(new ItemListener()
{
}
for (final AlignmentPanel ap : allviews)
{
- String nm = ((ap.getViewName() == null || ap.getViewName().length() == 0) ? ""
- : ap.getViewName() + " for ")
+ String nm = ((ap.getViewName() == null
+ || ap.getViewName().length() == 0) ? ""
+ : ap.getViewName() + " for ")
+ ap.alignFrame.getTitle();
final JCheckBoxMenuItem checkBox = new JCheckBoxMenuItem(nm,
_selectedviews.contains(ap));
* @author $author$
* @version $Revision$
*/
-public class WebserviceInfo extends GWebserviceInfo implements
- HyperlinkListener, IProgressIndicator
+public class WebserviceInfo extends GWebserviceInfo
+ implements HyperlinkListener, IProgressIndicator
{
/** Job is Queued */
this.title = title;
setInfoText(info);
- java.net.URL url = getClass().getResource(
- "/images/Jalview_Logo_small.png");
+ java.net.URL url = getClass()
+ .getResource("/images/Jalview_Logo_small.png");
image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
MediaTracker mt = new MediaTracker(this);
Thread thread = new Thread(ap);
thread.start();
final WebserviceInfo thisinfo = this;
- frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
- {
- public void internalFrameClosed(
- javax.swing.event.InternalFrameEvent evt)
- {
- // System.out.println("Shutting down webservice client");
- WSClientI service = thisinfo.getthisService();
- if (service != null && service.isCancellable())
- {
- service.cancelJob();
- }
- };
- });
+ frame.addInternalFrameListener(
+ new javax.swing.event.InternalFrameAdapter()
+ {
+ public void internalFrameClosed(
+ javax.swing.event.InternalFrameEvent evt)
+ {
+ // System.out.println("Shutting down webservice client");
+ WSClientI service = thisinfo.getthisService();
+ if (service != null && service.isCancellable())
+ {
+ service.cancelJob();
+ }
+ };
+ });
frame.validate();
}
if (jobpane < 0 || jobpane >= jobPanes.size())
{
throw new Error(MessageManager.formatMessage(
- "error.setstatus_called_non_existent_job_pane",
- new String[] { Integer.valueOf(jobpane).toString() }));
+ "error.setstatus_called_non_existent_job_pane", new String[]
+ { Integer.valueOf(jobpane).toString() }));
}
switch (status)
{
int htmlpos = leaveFirst ? -1 : lowertxt.indexOf("<body");
int htmlend = leaveLast ? -1 : lowertxt.indexOf("</body");
- int htmlpose = lowertxt.indexOf(">", htmlpos), htmlende = lowertxt
- .indexOf(">", htmlend);
+ int htmlpose = lowertxt.indexOf(">", htmlpos),
+ htmlende = lowertxt.indexOf(">", htmlend);
if (htmlend == -1 && htmlpos == -1)
{
return text;
}
if (text.indexOf("<meta") > -1)
{
- System.err.println("HTML COntent: \n" + text
- + "<< END HTML CONTENT\n");
+ System.err
+ .println("HTML COntent: \n" + text + "<< END HTML CONTENT\n");
}
return text;
{
String txt = getHtmlFragment(
((JEditorPane) ((JScrollPane) jobPanes.get(which))
- .getViewport().getComponent(0)).getText(), true,
- false);
+ .getViewport().getComponent(0)).getText(),
+ true, false);
((JEditorPane) ((JScrollPane) jobPanes.get(which)).getViewport()
- .getComponent(0)).setText(ensureHtmlTagged(txt
- + getHtmlFragment(text, false, true)));
+ .getComponent(0))
+ .setText(ensureHtmlTagged(
+ txt + getHtmlFragment(text, false, true)));
}
else
{
// JBPNote : TODO: Instead of a warning, we should have an optional 'Are
// you sure?' prompt
warnUser(
- MessageManager
- .getString("warn.job_cannot_be_cancelled_close_window"),
+ MessageManager.getString(
+ "warn.job_cannot_be_cancelled_close_window"),
MessageManager.getString("action.cancel_job"));
}
else
{
Thread.sleep(50);
- int units = (int) ((System.currentTimeMillis() - startTime) / 10f);
+ int units = (int) ((System.currentTimeMillis() - startTime)
+ / 10f);
angle += units;
angle %= 360;
startTime = System.currentTimeMillis();
case STATE_CANCELLED_OK:
g.drawString(
- title.concat(" - ").concat(
- MessageManager
+ title.concat(" - ")
+ .concat(MessageManager
.getString("label.state_job_cancelled")),
60, 30);
case STATE_STOPPED_SERVERERROR:
g.drawString(
- title.concat(" - ").concat(
- MessageManager
+ title.concat(" - ")
+ .concat(MessageManager
.getString("label.server_error_try_later")),
60, 30);
* @param jobArgset
*/
public WsJobParameters(JFrame parent, ParamDatastoreI paramStorei,
- Jws2Instance service, WsParamSetI preset, List<Argument> jobArgset)
+ Jws2Instance service, WsParamSetI preset,
+ List<Argument> jobArgset)
{
super();
jbInit();
frame = new JDialog(Desktop.instance, true);
frame.setTitle(MessageManager.formatMessage("label.edit_params_for",
- new String[] { service.getActionText() }));
+ new String[]
+ { service.getActionText() }));
Rectangle deskr = Desktop.instance.getBounds();
Dimension pref = this.getPreferredSize();
- frame.setBounds(new Rectangle(
- (int) (deskr.getCenterX() - pref.width / 2), (int) (deskr
- .getCenterY() - pref.height / 2), pref.width,
- pref.height));
+ frame.setBounds(
+ new Rectangle((int) (deskr.getCenterX() - pref.width / 2),
+ (int) (deskr.getCenterY() - pref.height / 2),
+ pref.width, pref.height));
frame.setContentPane(this);
// should perhaps recover defaults from user prefs.
create_actionPerformed(e);
}
});
- revertpref = JvSwingUtils.makeButton(MessageManager
- .getString("action.revert"), MessageManager
- .getString("label.revert_changes_user_parameter_set"),
+ revertpref = JvSwingUtils.makeButton(
+ MessageManager.getString("action.revert"),
+ MessageManager
+ .getString("label.revert_changes_user_parameter_set"),
new ActionListener()
{
}
});
- setDetails.setBorder(new TitledBorder(MessageManager
- .getString("label.details")));
+ setDetails.setBorder(
+ new TitledBorder(MessageManager.getString("label.details")));
setDetails.setLayout(new BorderLayout());
setDescr.setColumns(40);
setDescr.setWrapStyleWord(true);
setDescr.setBackground(getBackground());
setDescr.setEditable(true);
setDescr.getDocument().addDocumentListener(this);
- setDescr.setToolTipText(MessageManager
- .getString("label.edit_notes_parameter_set"));
+ setDescr.setToolTipText(
+ MessageManager.getString("label.edit_notes_parameter_set"));
JScrollPane setDescrView = new JScrollPane();
setDescrView.getViewport().setView(setDescr);
setName.setEditable(true);
// paramPane.setPreferredSize(new Dimension(360, 400));
// paramPane.setPreferredSize(null);
- jobOptions.setBorder(new TitledBorder(MessageManager
- .getString("label.options")));
+ jobOptions.setBorder(
+ new TitledBorder(MessageManager.getString("label.options")));
jobOptions.setOpaque(true);
- paramList.setBorder(new TitledBorder(MessageManager
- .getString("label.parameters")));
+ paramList.setBorder(
+ new TitledBorder(MessageManager.getString("label.parameters")));
paramList.setOpaque(true);
- JPanel bjo = new JPanel(new BorderLayout()), bjp = new JPanel(
- new BorderLayout());
+ JPanel bjo = new JPanel(new BorderLayout()),
+ bjp = new JPanel(new BorderLayout());
bjo.add(jobOptions, BorderLayout.CENTER);
bjp.add(paramList, BorderLayout.CENTER);
bjp.setOpaque(true);
List<ArgumentI> jobArgset = null;
settingDialog = true;
{ // instantiate the abstract proxy for Jaba objects
- jobArgset = jabajobArgset == null ? null : JabaParamStore
- .getJwsArgsfromJaba(jabajobArgset);
+ jobArgset = jabajobArgset == null ? null
+ : JabaParamStore.getJwsArgsfromJaba(jabajobArgset);
p = jabap; // (jabap != null) ? paramStore.getPreset(jabap.getName()) :
// null;
}
private void updateButtonDisplay()
{
- boolean _update = false, _create = false, _delete = false, _revert = false;
+ boolean _update = false, _create = false, _delete = false,
+ _revert = false;
if (modifiedElements.size() > 0)
{
// set modified
boolean stn = settingDialog;
boolean renamed = false;
settingDialog = true;
- String nm = (curSetName != null ? curSetName : (String) setName
- .getSelectedItem());
+ String nm = (curSetName != null ? curSetName
+ : (String) setName.getSelectedItem());
// check if the name is reserved - if it is, rename it.
if (isServicePreset(nm))
{
FlowLayout fl = new FlowLayout(FlowLayout.LEFT);
int sep = fl.getVgap();
boolean fh = true;
- int os = 0, s = jobOptions.getBorder().getBorderInsets(jobOptions).bottom
- + jobOptions.getBorder().getBorderInsets(jobOptions).top
- + 2
- * sep;
+ int os = 0,
+ s = jobOptions.getBorder().getBorderInsets(jobOptions).bottom
+ + jobOptions.getBorder().getBorderInsets(jobOptions).top
+ + 2 * sep;
/**
* final height for viewport
*/
- jobOptions.getBorder().getBorderInsets(jobOptions).left
+ jobOptions.getBorder().getBorderInsets(jobOptions).right;
- int w = 2
- * fl.getHgap()
+ int w = 2 * fl.getHgap()
+ (MAX_OPTWIDTH > OptsAndParamsPage.PARAM_WIDTH ? MAX_OPTWIDTH
: OptsAndParamsPage.PARAM_WIDTH);
int hgap = fl.getHgap(), cw = hgap;
}
{
System.out.println("Testing opts dupes for "
- + lastserv.getUri() + " : "
- + lastserv.getActionText() + ":" + pr.getName());
+ + lastserv.getUri() + " : " + lastserv.getActionText()
+ + ":" + pr.getName());
List<Option> rg = lastserv.getRunnerConfig().getOptions();
for (Option o : rg)
{
lastserv.getRunnerConfig(), " ");
readparam = jalview.ws.jws2.ParameterUtils
.writeParameterSet(pset, " ");
- Iterator<String> o = pr.getOptions().iterator(), s = writeparam
- .iterator(), t = readparam.iterator();
+ Iterator<String> o = pr.getOptions().iterator(),
+ s = writeparam.iterator(), t = readparam.iterator();
boolean failed = false;
while (s.hasNext() && t.hasNext())
{
String on = o.next(), sn = s.next(), st = t.next();
if (!sn.equals(st))
{
- System.out.println("Original was " + on
- + " Phase 1 wrote " + sn + "\tPhase 2 wrote "
- + st);
+ System.out.println(
+ "Original was " + on + " Phase 1 wrote " + sn
+ + "\tPhase 2 wrote " + st);
failed = true;
}
}
if (failed)
{
- System.out.println("Original parameters:\n"
- + pr.getOptions());
- System.out.println("Wrote parameters in first set:\n"
- + writeparam);
- System.out.println("Wrote parameters in second set:\n"
- + readparam);
+ System.out.println(
+ "Original parameters:\n" + pr.getOptions());
+ System.out.println(
+ "Wrote parameters in first set:\n" + writeparam);
+ System.out.println(
+ "Wrote parameters in second set:\n" + readparam);
}
} catch (Exception e)
}
WsJobParameters pgui = new WsJobParameters(lastserv,
new JabaPreset(lastserv, pr));
- JFrame jf = new JFrame(MessageManager.formatMessage(
- "label.ws_parameters_for",
- new String[] { lastserv.getActionText() }));
+ JFrame jf = new JFrame(MessageManager
+ .formatMessage("label.ws_parameters_for", new String[]
+ { lastserv.getActionText() }));
JPanel cont = new JPanel(new BorderLayout());
pgui.validate();
cont.setPreferredSize(pgui.getPreferredSize());
public boolean isServiceDefaults()
{
- return (!isModified() && (lastParmSet != null && lastParmSet
- .equals(SVC_DEF)));
+ return (!isModified()
+ && (lastParmSet != null && lastParmSet.equals(SVC_DEF)));
}
public List<ArgumentI> getJobParams()
}
settingDialog = true;
System.out.println("Prompting to save " + lsetname);
- if (JvOptionPane
- .showConfirmDialog(
- this,
- "Parameter set '"
- + lsetname
- + "' is modifed, and your changes will be lost.\nReally change preset ?",
- "Warning: Unsaved Changes",
- JvOptionPane.OK_CANCEL_OPTION) != JvOptionPane.OK_OPTION)
+ if (JvOptionPane.showConfirmDialog(this, "Parameter set '" + lsetname
+ + "' is modifed, and your changes will be lost.\nReally change preset ?",
+ "Warning: Unsaved Changes",
+ JvOptionPane.OK_CANCEL_OPTION) != JvOptionPane.OK_OPTION)
{
// revert the combobox to the current item
settingDialog = true;
@Override
public void run()
{
- JvOptionPane.showMessageDialog(ourframe, MessageManager
- .getString("label.invalid_name_preset_exists"),
+ JvOptionPane.showMessageDialog(ourframe,
+ MessageManager.getString(
+ "label.invalid_name_preset_exists"),
MessageManager.getString("label.invalid_name"),
JvOptionPane.WARNING_MESSAGE);
}
if (!settingDialog)
{
- argSetModified(
- setDescr,
- (lastDescrText == null ? setDescr.getText().trim().length() > 0
+ argSetModified(setDescr,
+ (lastDescrText == null
+ ? setDescr.getText().trim().length() > 0
: !setDescr.getText().equals(lastDescrText)));
}
{
add = true;
}
- add &= (modifiable == p.isModifiable() || unmodifiable == !p
- .isModifiable());
+ add &= (modifiable == p.isModifiable()
+ || unmodifiable == !p.isModifiable());
add &= name == null || p.getName().equals(name);
if (add)
}
} catch (IOException e)
{
- Cache.log
- .info("Failed to parse parameter file "
- + pfile
- + " (Check that all JALVIEW_WSPARAMFILES entries are valid!)",
- e);
+ Cache.log.info("Failed to parse parameter file " + pfile
+ + " (Check that all JALVIEW_WSPARAMFILES entries are valid!)",
+ e);
}
}
return params.toArray(new WsParamSetI[0]);
}
if (parser == null)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_cannot_find_marshaller_for_param_set"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_cannot_find_marshaller_for_param_set"));
}
if (filename == null)
{
if (value == JalviewFileChooser.APPROVE_OPTION)
{
outfile = chooser.getSelectedFile();
- jalview.bin.Cache
- .setProperty("LAST_DIRECTORY", outfile.getParent());
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+ outfile.getParent());
filename = outfile.getAbsolutePath();
if (!filename.endsWith(".wsparams"))
{
paramxml.setVersion("1.0");
try
{
- paramxml.setParameters(parser
- .generateServiceParameterFile(parameterSet));
+ paramxml.setParameters(
+ parser.generateServiceParameterFile(parameterSet));
PrintWriter out = new PrintWriter(new OutputStreamWriter(
new FileOutputStream(outfile), "UTF-8"));
paramxml.marshal(out);
}
} catch (Exception e)
{
- Cache.log
- .error("Exception when trying to delete webservice user preset: ",
- e);
+ Cache.log.error(
+ "Exception when trying to delete webservice user preset: ",
+ e);
}
}
rsbsUrls = new Vector<String>();
}
updateRsbsList();
- enableEnfinServices.setSelected(oldEnfin = Cache.getDefault(
- "SHOW_ENFIN_SERVICES", true));
+ enableEnfinServices.setSelected(
+ oldEnfin = Cache.getDefault("SHOW_ENFIN_SERVICES", true));
enableEnfinServices.addActionListener(updateAction);
- enableJws2Services.setSelected(oldJws2 = Cache.getDefault(
- "SHOW_JWS2_SERVICES", true));
+ enableJws2Services.setSelected(
+ oldJws2 = Cache.getDefault("SHOW_JWS2_SERVICES", true));
enableJws2Services.addActionListener(updateAction);
- indexByHost.setSelected(oldIndexByHost = Cache.getDefault(
- "WSMENU_BYHOST", false));
+ indexByHost.setSelected(
+ oldIndexByHost = Cache.getDefault("WSMENU_BYHOST", false));
indexByHost.addActionListener(updateAction);
- indexByType.setSelected(oldIndexByType = Cache.getDefault(
- "WSMENU_BYTYPE", false));
+ indexByType.setSelected(
+ oldIndexByType = Cache.getDefault("WSMENU_BYTYPE", false));
indexByType.addActionListener(updateAction);
- displayWsWarning.setSelected(oldWsWarning = Cache.getDefault(
- "SHOW_WSDISCOVERY_ERRORS", true));
+ displayWsWarning.setSelected(oldWsWarning = Cache
+ .getDefault("SHOW_WSDISCOVERY_ERRORS", true));
}
ActionListener updateAction = new ActionListener()
}
wsList.setModel(new WsUrlTableModel(tdat));
- wsList.getColumn(MessageManager.getString("label.status")).setMinWidth(
- 10);
+ wsList.getColumn(MessageManager.getString("label.status"))
+ .setMinWidth(10);
}
- private class JabaWSStatusRenderer extends JPanel implements
- TableCellRenderer
+ private class JabaWSStatusRenderer extends JPanel
+ implements TableCellRenderer
{
public JabaWSStatusRenderer()
{
{
if (old)
{
- if (oldUrls != wsUrls
- || (wsUrls != null && oldUrls != null && !wsUrls
- .equals(oldUrls)))
+ if (oldUrls != wsUrls || (wsUrls != null && oldUrls != null
+ && !wsUrls.equals(oldUrls)))
{
update++;
}
wsUrls = (oldUrls == null) ? null : new Vector(oldUrls);
- if (oldRsbsUrls != rsbsUrls
- || (rsbsUrls != null && oldRsbsUrls != null && !oldRsbsUrls
- .equals(rsbsUrls)))
+ if (oldRsbsUrls != rsbsUrls || (rsbsUrls != null
+ && oldRsbsUrls != null && !oldRsbsUrls.equals(rsbsUrls)))
{
update++;
}
{
}
- Cache.setProperty(
- "SHOW_ENFIN_SERVICES",
+ Cache.setProperty("SHOW_ENFIN_SERVICES",
Boolean.valueOf(
old ? oldEnfin : enableEnfinServices.isSelected())
.toString());
- Cache.setProperty(
- "SHOW_JWS2_SERVICES",
+ Cache.setProperty("SHOW_JWS2_SERVICES",
Boolean.valueOf(old ? oldJws2 : enableJws2Services.isSelected())
.toString());
- Cache.setProperty(
- "WSMENU_BYHOST",
+ Cache.setProperty("WSMENU_BYHOST",
Boolean.valueOf(old ? oldIndexByHost : indexByHost.isSelected())
.toString());
- Cache.setProperty(
- "WSMENU_BYTYPE",
+ Cache.setProperty("WSMENU_BYTYPE",
Boolean.valueOf(old ? oldIndexByType : indexByType.isSelected())
.toString());
- Cache.setProperty(
- "SHOW_WSDISCOVERY_ERRORS",
+ Cache.setProperty("SHOW_WSDISCOVERY_ERRORS",
Boolean.valueOf(
old ? oldWsWarning : displayWsWarning.isSelected())
.toString());
panel.add(pane12, BorderLayout.NORTH);
boolean valid = false;
int resp = JvOptionPane.CANCEL_OPTION;
- while (!valid
- && (resp = JvOptionPane.showInternalConfirmDialog(
- Desktop.desktop, panel, title,
- JvOptionPane.OK_CANCEL_OPTION)) == JvOptionPane.OK_OPTION)
+ while (!valid && (resp = JvOptionPane.showInternalConfirmDialog(
+ Desktop.desktop, panel, title,
+ JvOptionPane.OK_CANCEL_OPTION)) == JvOptionPane.OK_OPTION)
{
try
{
}
else
{
- int opt = JvOptionPane
- .showInternalOptionDialog(
- Desktop.desktop,
- "The Server '"
- + foo.toString()
- + "' failed validation,\ndo you want to add it anyway? ",
- "Server Validation Failed",
- JvOptionPane.YES_NO_OPTION,
- JvOptionPane.INFORMATION_MESSAGE, null, null, null);
+ int opt = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
+ "The Server '" + foo.toString()
+ + "' failed validation,\ndo you want to add it anyway? ",
+ "Server Validation Failed", JvOptionPane.YES_NO_OPTION,
+ JvOptionPane.INFORMATION_MESSAGE, null, null, null);
if (opt == JvOptionPane.YES_OPTION)
{
return foo.toString();
}
else
{
- JvOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- MessageManager
- .getString("warn.server_didnt_pass_validation"));
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString(
+ "warn.server_didnt_pass_validation"));
}
}
/*
* Can't write an HTTP header once any response content has been written
*/
- System.err
- .println("Unable to return HTTP 500 as response already committed");
+ System.err.println(
+ "Unable to return HTTP 500 as response already committed");
}
else
{
stop();
} catch (Exception e)
{
- System.err.println("Error stopping " + getName() + ": "
- + e.getMessage());
+ System.err.println(
+ "Error stopping " + getName() + ": " + e.getMessage());
}
}
contextRoot = server.getURI();
} catch (Exception e)
{
- System.err.println("Error trying to start HttpServer: "
- + e.getMessage());
+ System.err.println(
+ "Error trying to start HttpServer: " + e.getMessage());
try
{
server.stop();
ch.start();
} catch (Exception e)
{
- System.err.println("Error starting handler for " + path + ": "
- + e.getMessage());
+ System.err.println(
+ "Error starting handler for " + path + ": " + e.getMessage());
}
handler.setUri(this.contextRoot + ch.getContextPath().substring(1));
* @author $author$
* @version $Revision$
*/
-public abstract class AlignFile extends FileParse implements
- AlignmentFileReaderI, AlignmentFileWriterI
+public abstract class AlignFile extends FileParse
+ implements AlignmentFileReaderI, AlignmentFileWriterI
{
int noSeqs = 0;
* @throws IOException
*/
public AlignFile(boolean parseImmediately, String dataObject,
- DataSourceType sourceType)
- throws IOException
+ DataSourceType sourceType) throws IOException
{
super(dataObject, sourceType);
initData();
{
if (key == null)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_cannot_have_null_alignment"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_cannot_have_null_alignment"));
}
if (value == null)
{
public String printAnnotations(AlignmentAnnotation[] annotations,
List<SequenceGroup> list, Hashtable properties)
{
- return printAnnotations(annotations, list, properties, null, null, null);
+ return printAnnotations(annotations, list, properties, null, null,
+ null);
}
public final Hashtable hiddenRepSeqs;
- public ViewDef(String vname, HiddenSequences hseqs,
- HiddenColumns hcols, Hashtable hRepSeqs)
+ public ViewDef(String vname, HiddenSequences hseqs, HiddenColumns hcols,
+ Hashtable hRepSeqs)
{
this.viewname = vname;
this.hidseqs = hseqs;
* @return annotation file
*/
public String printAnnotations(AlignmentAnnotation[] annotations,
- List<SequenceGroup> list, Hashtable properties,
- HiddenColumns cs,
+ List<SequenceGroup> list, Hashtable properties, HiddenColumns cs,
AlignmentI al, ViewDef view)
{
if (view != null)
{
row = annotations[i];
- if (!row.visible
- && !row.hasScore()
- && !(row.graphGroup > -1 && graphGroupSeen
- .get(row.graphGroup)))
+ if (!row.visible && !row.hasScore() && !(row.graphGroup > -1
+ && graphGroupSeen.get(row.graphGroup)))
{
continue;
}
writeGroup_Ref(refGroup, row.groupRef);
refGroup = row.groupRef;
- boolean hasGlyphs = row.hasIcons, hasLabels = row.hasText, hasValues = row.hasScore, hasText = false;
+ boolean hasGlyphs = row.hasIcons, hasLabels = row.hasText,
+ hasValues = row.hasScore, hasText = false;
// lookahead to check what the annotation row object actually contains.
for (int j = 0; row.annotations != null
&& j < row.annotations.length
if (row.annotations[j] != null)
{
hasLabels |= (row.annotations[j].displayCharacter != null
- && row.annotations[j].displayCharacter.length() > 0 && !row.annotations[j].displayCharacter
- .equals(" "));
- hasGlyphs |= (row.annotations[j].secondaryStructure != 0 && row.annotations[j].secondaryStructure != ' ');
+ && row.annotations[j].displayCharacter.length() > 0
+ && !row.annotations[j].displayCharacter.equals(" "));
+ hasGlyphs |= (row.annotations[j].secondaryStructure != 0
+ && row.annotations[j].secondaryStructure != ' ');
hasValues |= (!Float.isNaN(row.annotations[j].value)); // NaNs can't
// be
// rendered..
- hasText |= (row.annotations[j].description != null && row.annotations[j].description
- .length() > 0);
+ hasText |= (row.annotations[j].description != null
+ && row.annotations[j].description.length() > 0);
}
}
graphLine.append("\t");
graphLine.append(row.getThreshold().label);
graphLine.append("\t");
- graphLine.append(jalview.util.Format.getHexString(row
- .getThreshold().colour));
+ graphLine.append(jalview.util.Format
+ .getHexString(row.getThreshold().colour));
graphLine.append(newline);
}
if (row.annotations[j].colour != null
&& row.annotations[j].colour != java.awt.Color.black)
{
- text.append(comma
- + "["
- + jalview.util.Format
- .getHexString(row.annotations[j].colour)
- + "]");
+ text.append(comma + "[" + jalview.util.Format
+ .getHexString(row.annotations[j].colour) + "]");
comma = ",";
}
}
for (Map.Entry<Integer, String> combine_statement : graphGroup
.entrySet())
{
- Object[] seqRefAndGroup = graphGroup_refs.get(combine_statement
- .getKey());
+ Object[] seqRefAndGroup = graphGroup_refs
+ .get(combine_statement.getKey());
writeSequence_Ref(refSeq, (SequenceI) seqRefAndGroup[0]);
refSeq = (SequenceI) seqRefAndGroup[0];
if (sg.cs != null)
{
text.append("colour=");
- text.append(ColourSchemeProperty.getColourName(sg.cs
- .getColourScheme()));
+ text.append(ColourSchemeProperty
+ .getColourName(sg.cs.getColourScheme()));
text.append("\t");
if (sg.cs.getThreshold() != 0)
{
String refSeqId = null;
- public boolean annotateAlignmentView(AlignViewportI viewport,
- String file, DataSourceType protocol)
+ public boolean annotateAlignmentView(AlignViewportI viewport, String file,
+ DataSourceType protocol)
{
ColumnSelection colSel = viewport.getColumnSelection();
HiddenColumns hidden = viewport.getAlignment().getHiddenColumns();
{
hidden = new HiddenColumns();
}
- boolean rslt = readAnnotationFile(viewport.getAlignment(), hidden,
- file, protocol);
+ boolean rslt = readAnnotationFile(viewport.getAlignment(), hidden, file,
+ protocol);
if (rslt && (colSel.hasSelectedColumns() || hidden.hasHiddenColumns()))
{
viewport.setColumnSelection(colSel);
System.out.println("Problem reading annotation file: " + ex);
if (nlinesread > 0)
{
- System.out.println("Last read line " + nlinesread + ": '"
- + lastread + "' (first 80 chars) ...");
+ System.out.println("Last read line " + nlinesread + ": '" + lastread
+ + "' (first 80 chars) ...");
}
return false;
}
{
// keep a record of current state and resolve groupRef at end
combineAnnotation_calls
- .add(new Object[] { st, refSeq, groupRef });
+ .add(new Object[]
+ { st, refSeq, groupRef });
modified = true;
continue;
}
else if (token.equalsIgnoreCase(GRAPHLINE))
{
// resolve at end
- deferredAnnotation_calls.add(new Object[] { GRAPHLINE, st,
- refSeq, groupRef });
+ deferredAnnotation_calls
+ .add(new Object[]
+ { GRAPHLINE, st, refSeq, groupRef });
modified = true;
continue;
}
if (refSeqIndex < 1)
{
refSeqIndex = 1;
- System.out
- .println("WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile");
+ System.out.println(
+ "WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile");
}
} catch (Exception ex)
{
{
if (hidden == null)
{
- System.err
- .println("Cannot process HIDE_INSERTIONS without an alignment view: Ignoring line: "
+ System.err.println(
+ "Cannot process HIDE_INSERTIONS without an alignment view: Ignoring line: "
+ line);
}
else
(index == 0) ? null : annotations, 0, 0, graphStyle);
annotation.score = score;
- if (!overrideAutoAnnot
- && autoAnnots.containsKey(autoAnnotsKey(annotation, refSeq,
- groupRef)))
+ if (!overrideAutoAnnot && autoAnnots
+ .containsKey(autoAnnotsKey(annotation, refSeq, groupRef)))
{
// skip - we've already got an automatic annotation of this type.
continue;
// TODO: verify that undo/redo with 1:many sequence associated
// annotations can be undone correctly
AlignmentAnnotation ann = new AlignmentAnnotation(annotation);
- annotation
- .createSequenceMapping(referedSeq, refSeqIndex, false);
+ annotation.createSequenceMapping(referedSeq, refSeqIndex,
+ false);
annotation.adjustForAlignment();
referedSeq.addAlignmentAnnotation(annotation);
al.addAnnotation(annotation);
al.setAnnotationIndex(annotation,
- al.getAlignmentAnnotation().length
- - existingAnnotations - 1);
+ al.getAlignmentAnnotation().length - existingAnnotations
+ - 1);
if (groupRef != null)
{
((Vector) groupRefRows.get(groupRef)).addElement(annotation);
// and recover our virgin copy to use again if necessary.
annotation = ann;
- } while (refSeqId != null
- && (referedSeq = al.findName(referedSeq, refSeqId, true)) != null);
+ } while (refSeqId != null && (referedSeq = al.findName(referedSeq,
+ refSeqId, true)) != null);
}
else
{
{
// TODO: specify and implement duplication of alignment annotation
// for multiple group references.
- System.err
- .println("Ignoring 1:many group reference mappings for group name '"
+ System.err.println(
+ "Ignoring 1:many group reference mappings for group name '"
+ groupRef + "'");
}
else
if (rowset != null && rowset.size() > 0)
{
AlignmentAnnotation alan = null;
- for (int elm = 0, elmSize = rowset.size(); elm < elmSize; elm++)
+ for (int elm = 0, elmSize = rowset
+ .size(); elm < elmSize; elm++)
{
alan = (AlignmentAnnotation) rowset.elementAt(elm);
alan.groupRef = theGroup;
{
if (_deferred_args[0] == GRAPHLINE)
{
- addLine(al,
- (StringTokenizer) _deferred_args[1], // st
+ addLine(al, (StringTokenizer) _deferred_args[1], // st
(SequenceI) _deferred_args[2], // refSeq
- (_deferred_args[3] == null) ? null : groupRefLookup
- .get(_deferred_args[3]) // the reference
- // group, or null
+ (_deferred_args[3] == null) ? null
+ : groupRefLookup.get(_deferred_args[3]) // the
+ // reference
+ // group, or
+ // null
);
}
}
int combinecount = 0;
for (Object[] _combine_args : combineAnnotation_calls)
{
- combineAnnotations(al,
- ++combinecount,
+ combineAnnotations(al, ++combinecount,
(StringTokenizer) _combine_args[0], // st
(SequenceI) _combine_args[1], // refSeq
- (_combine_args[2] == null) ? null : groupRefLookup
- .get(_combine_args[2]) // the reference group,
- // or null
+ (_combine_args[2] == null) ? null
+ : groupRefLookup.get(_combine_args[2]) // the reference
+ // group,
+ // or null
);
}
}
int j = string.indexOf("]");
if (i > -1 && j > -1)
{
- colour = ColorUtils.parseColourString(string.substring(i + 1,
- j));
+ colour = ColorUtils.parseColourString(string.substring(i + 1, j));
if (i > 0 && string.charAt(i - 1) == ',')
{
// clip the preceding comma as well
displayChar = token;
}
}
- if (hasSymbols
- && (token.length() == 1 && "()<>[]{}AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz"
+ if (hasSymbols && (token.length() == 1
+ && "()<>[]{}AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz"
.contains(token)))
{
// Either this character represents a helix or sheet
}
else
{
- System.err
- .println("Couldn't combine annotations. None are added to alignment yet!");
+ System.err.println(
+ "Couldn't combine annotations. None are added to alignment yet!");
}
}
}
} catch (Exception e)
{
- System.err
- .println("Couldn't parse Group Start or End Field as '*' or a valid column or sequence index: '"
+ System.err.println(
+ "Couldn't parse Group Start or End Field as '*' or a valid column or sequence index: '"
+ rng + "' - assuming alignment width for group.");
// assume group is full width
sg.setStartRes(0);
}
else
{
- sg.addSequence(al.getSequenceAt(Integer.parseInt(tmp) - 1), false);
+ sg.addSequence(al.getSequenceAt(Integer.parseInt(tmp) - 1),
+ false);
}
}
}
}
else if (key.equalsIgnoreCase("colour"))
{
- sg.cs.setColourScheme(ColourSchemeProperty
- .getColourScheme(al, value));
+ sg.cs.setColourScheme(
+ ColourSchemeProperty.getColourScheme(al, value));
}
else if (key.equalsIgnoreCase("pidThreshold"))
{
AlignmentAnnotation aa, ala[] = al.getAlignmentAnnotation();
if (ala == null)
{
- System.err
- .print("Warning - no annotation to set below for sequence associated annotation:");
+ System.err.print(
+ "Warning - no annotation to set below for sequence associated annotation:");
}
while (st.hasMoreTokens())
{
public String printAnnotationsForView(AlignViewportI viewport)
{
- return printAnnotations(viewport.isShowAnnotation() ? viewport
- .getAlignment().getAlignmentAnnotation() : null, viewport
- .getAlignment().getGroups(), viewport.getAlignment()
- .getProperties(), viewport.getAlignment().getHiddenColumns(),
+ return printAnnotations(
+ viewport.isShowAnnotation()
+ ? viewport.getAlignment().getAlignmentAnnotation()
+ : null,
+ viewport.getAlignment().getGroups(),
+ viewport.getAlignment().getProperties(),
+ viewport.getAlignment().getHiddenColumns(),
viewport.getAlignment(), null);
}
public static String getSupportedFormats()
{
return "Formats currently supported are\n"
- + prettyPrint(FileFormats.getInstance().getReadableFormats());
+ + prettyPrint(FileFormats.getInstance().getReadableFormats());
}
+
public AppletFormatAdapter()
{
}
String structureParser = StructureImportSettings
.getDefaultPDBFileParser();
boolean isParseWithJMOL = structureParser.equalsIgnoreCase(
- StructureImportSettings.StructureParser.JMOL_PARSER
- .toString());
+ StructureImportSettings.StructureParser.JMOL_PARSER
+ .toString());
StructureImportSettings.addSettings(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct);
if (isParseWithJMOL)
localSecondaryStruct, serviceSecondaryStruct, inFile,
sourceType);
}
- ((StructureFile) alignFile).setDbRefType(FileFormat.PDB
- .equals(fileFormat) ? Type.PDB : Type.MMCIF);
+ ((StructureFile) alignFile).setDbRefType(
+ FileFormat.PDB.equals(fileFormat) ? Type.PDB : Type.MMCIF);
}
else
{
// alignFile = fileFormat.getAlignmentFile(inFile, sourceType);
- alignFile = fileFormat.getReader(new FileParse(inFile,
- sourceType));
+ alignFile = fileFormat.getReader(new FileParse(inFile, sourceType));
}
return buildAlignmentFromFile();
} catch (Exception e)
{
e.printStackTrace();
- System.err.println("Failed to read alignment using the '"
- + fileFormat + "' reader.\n" + e);
+ System.err.println("Failed to read alignment using the '" + fileFormat
+ + "' reader.\n" + e);
if (e.getMessage() != null
&& e.getMessage().startsWith(INVALID_CHARACTERS))
AlignmentViewPanel ap, boolean selectedOnly)
{
- AlignmentView selvew = ap.getAlignViewport().getAlignmentView(
- selectedOnly, false);
- AlignmentI aselview = selvew.getVisibleAlignment(ap.getAlignViewport()
- .getGapCharacter());
+ AlignmentView selvew = ap.getAlignViewport()
+ .getAlignmentView(selectedOnly, false);
+ AlignmentI aselview = selvew
+ .getVisibleAlignment(ap.getAlignViewport().getGapCharacter());
List<AlignmentAnnotation> ala = (ap.getAlignViewport()
.getVisibleAlignmentAnnotation(selectedOnly));
if (ala != null)
} catch (Exception e)
{
System.err.println("Failed to write alignment as a '"
- + format.getName()
- + "' file\n");
+ + format.getName() + "' file\n");
e.printStackTrace();
}
System.gc();
long memf = -r.totalMemory() + r.freeMemory();
long t1 = -System.currentTimeMillis();
- AlignmentI al = afa
- .readFile(args[i], DataSourceType.FILE,
- new IdentifyFile().identify(args[i],
- DataSourceType.FILE));
+ AlignmentI al = afa.readFile(args[i], DataSourceType.FILE,
+ new IdentifyFile().identify(args[i],
+ DataSourceType.FILE));
t1 += System.currentTimeMillis();
System.gc();
memf += r.totalMemory() - r.freeMemory();
+ " sequences and " + al.getWidth() + " columns.");
try
{
- System.out.println(new AppletFormatAdapter().formatSequences(
- FileFormat.Fasta, al, true));
+ System.out.println(new AppletFormatAdapter()
+ .formatSequences(FileFormat.Fasta, al, true));
} catch (Exception e)
{
- System.err
- .println("Couln't format the alignment for output as a FASTA file.");
+ System.err.println(
+ "Couln't format the alignment for output as a FASTA file.");
e.printStackTrace(System.err);
}
}
System.out.println("Couldn't read alignment");
}
System.out.println("Read took " + (t1 / 1000.0) + " seconds.");
- System.out
- .println("Difference between free memory now and before is "
+ System.out.println(
+ "Difference between free memory now and before is "
+ (memf / (1024.0 * 1024.0) * 1.0) + " MB");
} catch (Exception e)
{
{
if (debug)
{
- System.out.println("Trying to get contents of resource as "
- + protocol + ":");
+ System.out.println(
+ "Trying to get contents of resource as " + protocol + ":");
}
fp = new FileParse(file, protocol);
if (!fp.isValid())
.getDefault("biojs_template_directory", DEFAULT_DIR);
public static final String BJS_TEMPLATE_GIT_REPO = jalview.bin.Cache
- .getDefault(
- "biojs_template_git_repo",
+ .getDefault("biojs_template_git_repo",
"https://raw.githubusercontent.com/jalview/exporter-templates/master/biojs/package.json");
public BioJsHTMLOutput(AlignmentPanel ap)
return;
} catch (Exception e)
{
- setProgressMessage(MessageManager.formatMessage(
- "info.error_creating_file", "BioJS MSA"));
+ setProgressMessage(MessageManager
+ .formatMessage("info.error_creating_file", "BioJS MSA"));
e.printStackTrace();
return;
}
}
-
-
public static void refreshVersionInfo(String dirName)
throws URISyntaxException
{
{
try
{
- String gitRepoPkgJson = getURLContentAsString(BJS_TEMPLATE_GIT_REPO);
+ String gitRepoPkgJson = getURLContentAsString(
+ BJS_TEMPLATE_GIT_REPO);
if (gitRepoPkgJson != null)
{
BioJSRepositoryPojo release = new BioJSRepositoryPojo(
}
}
}
- return responseStrBuilder == null ? null : responseStrBuilder
- .toString();
+ return responseStrBuilder == null ? null
+ : responseStrBuilder.toString();
}
public static File getCurrentBJSTemplateFile()
String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
.replaceAll("#sequenceData#", bioJSON).toString();
- PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
- generatedFile));
+ PrintWriter out = new java.io.PrintWriter(
+ new java.io.FileWriter(generatedFile));
out.print(generatedBioJsWithJalviewAlignmentAsJson);
out.flush();
out.close();
- setProgressMessage(MessageManager.formatMessage(
- "status.export_complete", "BioJS"));
+ setProgressMessage(MessageManager
+ .formatMessage("status.export_complete", "BioJS"));
exportCompleted();
} catch (OutOfMemoryError err)
new OOMWarning("Creating Image for " + generatedFile, err);
} catch (Exception e)
{
- setProgressMessage(MessageManager.formatMessage(
- "info.error_creating_file", "HTML"));
+ setProgressMessage(MessageManager
+ .formatMessage("info.error_creating_file", "HTML"));
e.printStackTrace();
}
boolean flag = false;
boolean rna = false;
boolean top = false;
- StringBuffer pssecstr = new StringBuffer(), consstr = new StringBuffer();
+ StringBuffer pssecstr = new StringBuffer(),
+ consstr = new StringBuffer();
Vector headers = new Vector();
Hashtable seqhash = new Hashtable();
StringBuffer tempseq;
}
Sequence newSeq = parseId(headers.elementAt(i).toString());
- newSeq.setSequence(seqhash.get(headers.elementAt(i).toString())
- .toString());
+ newSeq.setSequence(
+ seqhash.get(headers.elementAt(i).toString()).toString());
seqs.addElement(newSeq);
}
else
{
- System.err
- .println("Clustal File Reader: Can't find sequence for "
- + headers.elementAt(i));
+ System.err.println("Clustal File Reader: Can't find sequence for "
+ + headers.elementAt(i));
}
}
AlignmentAnnotation lastssa = null;
AlignmentAnnotation ssa = StockholmFile.parseAnnotationRow(ss,
"secondary structure", consstr.toString());
ssa.label = "Consensus Secondary Structure";
- if (lastssa == null
- || !lastssa.getRNAStruc().equals(
- ssa.getRNAStruc().replace('-', '.')))
+ if (lastssa == null || !lastssa.getRNAStruc()
+ .equals(ssa.getRNAStruc().replace('-', '.')))
{
annotations.addElement(ssa);
}
while ((j < s.length) && (s[j] != null))
{
- out.append(new Format("%-" + maxid + "s").form(printId(s[j],
- jvsuffix) + " "));
+ out.append(new Format("%-" + maxid + "s")
+ .form(printId(s[j], jvsuffix) + " "));
int start = i * len;
int end = start + len;
anots[i] = new Annotation("" + cn, null, ' ', Float.NaN);
}
}
- AlignmentAnnotation aa = new AlignmentAnnotation(seq.getName()
- .substring(2), seq.getDescription(), anots);
+ AlignmentAnnotation aa = new AlignmentAnnotation(
+ seq.getName().substring(2), seq.getDescription(), anots);
return aa;
}
* @throws IOException
*/
public FeaturesFile(boolean parseImmediately, String inFile,
- DataSourceType type)
- throws IOException
+ DataSourceType type) throws IOException
{
super(parseImmediately, inFile, type);
}
*/
protected boolean parseJalviewFeature(String line, String[] gffColumns,
AlignmentI alignment, Map<String, FeatureColourI> featureColours,
- boolean removeHTML, boolean relaxedIdMatching, String featureGroup)
+ boolean removeHTML, boolean relaxedIdMatching,
+ String featureGroup)
{
/*
* tokens: description seqid seqIndex start end type [score]
Color colour = ColorUtils.createColourFromName(ft);
featureColours.put(ft, new FeatureColour(colour));
}
- SequenceFeature sf = new SequenceFeature(ft, desc, "", startPos,
- endPos, featureGroup);
+ SequenceFeature sf = new SequenceFeature(ft, desc, "", startPos, endPos,
+ featureGroup);
if (gffColumns.length > 6)
{
float score = Float.NaN;
for (int j = 0; j < features.length; j++)
{
isnonpos = features[j].begin == 0 && features[j].end == 0;
- if ((!nonpos && isnonpos)
- || (!isnonpos && visOnly && !visible
- .containsKey(features[j].type)))
+ if ((!nonpos && isnonpos) || (!isnonpos && visOnly
+ && !visible.containsKey(features[j].type)))
{
continue;
}
{
isnonpos = sequenceFeature.begin == 0
&& sequenceFeature.end == 0;
- if ((!nonpos && isnonpos)
- || (!isnonpos && visOnly && !visible
- .containsKey(sequenceFeature.type)))
+ if ((!nonpos && isnonpos) || (!isnonpos && visOnly
+ && !visible.containsKey(sequenceFeature.type)))
{
// skip if feature is nonpos and we ignore them or if we only
// output visible and it isn't non-pos and it's not visible
continue;
}
- if (group != null
- && (sequenceFeature.featureGroup == null || !sequenceFeature.featureGroup
- .equals(group)))
+ if (group != null && (sequenceFeature.featureGroup == null
+ || !sequenceFeature.featureGroup.equals(group)))
{
continue;
}
}
else
{
- if (sequenceFeature.links != null
- && sequenceFeature.getDescription().indexOf("<html>") == -1)
+ if (sequenceFeature.links != null && sequenceFeature
+ .getDescription().indexOf("<html>") == -1)
{
out.append("<html>");
}
if (sequenceFeature.description.indexOf(href) == -1)
{
- out.append(" <a href=\"" + href + "\">" + label
- + "</a>");
+ out.append(
+ " <a href=\"" + href + "\">" + label + "</a>");
}
}
- if (sequenceFeature.getDescription().indexOf("</html>") == -1)
+ if (sequenceFeature.getDescription()
+ .indexOf("</html>") == -1)
{
out.append("</html>");
}
fromCount = Integer.parseInt(tokens[2]);
} catch (NumberFormatException nfe)
{
- throw new IOException("Invalid number in Align field: "
- + nfe.getMessage());
+ throw new IOException(
+ "Invalid number in Align field: " + nfe.getMessage());
}
/*
* @param newseqs
* @throws IOException
*/
- protected void processGffPragma(String line,
- Map<String, String> gffProps, AlignmentI align,
- List<SequenceI> newseqs) throws IOException
+ protected void processGffPragma(String line, Map<String, String> gffProps,
+ AlignmentI align, List<SequenceI> newseqs) throws IOException
{
line = line.trim();
if ("###".equals(line))
@Override
public void run()
{
- String title = protocol == DataSourceType.PASTE ? "Copied From Clipboard"
+ String title = protocol == DataSourceType.PASTE
+ ? "Copied From Clipboard"
: file;
Runtime rt = Runtime.getRuntime();
try
+ "\" has null or unidentifiable data content!");
if (!Jalview.isHeadlessMode())
{
- JvOptionPane.showInternalMessageDialog(
- Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.getString("label.couldnt_read_data")
+ " in " + file + "\n"
+ AppletFormatAdapter.getSupportedFormats(),
if (source != null)
{
// Tell the user (developer?) that this is going to cause a problem
- System.err
- .println("IMPLEMENTATION ERROR: Cannot read consecutive Jalview XML projects from a stream.");
+ System.err.println(
+ "IMPLEMENTATION ERROR: Cannot read consecutive Jalview XML projects from a stream.");
// We read the data anyway - it might make sense.
}
alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(file);
if (downloadStructureFile)
{
String structExt = format.getExtensions().split(",")[0];
- String urlLeafName = file.substring(file.lastIndexOf(System
- .getProperty("file.separator")), file
- .lastIndexOf("."));
+ String urlLeafName = file.substring(
+ file.lastIndexOf(
+ System.getProperty("file.separator")),
+ file.lastIndexOf("."));
String tempStructureFileStr = createNamedJvTempFile(
urlLeafName, structExt);
UrlDownloadClient.download(file, tempStructureFileStr);
{
// register PDB entries with desktop's structure selection
// manager
- StructureSelectionManager.getStructureSelectionManager(
- Desktop.instance).registerPDBEntry(pdbe);
+ StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance)
+ .registerPDBEntry(pdbe);
}
}
}
alignFrame.getViewport().setFeaturesDisplayed(fd);
alignFrame.getViewport().setShowSequenceFeatures(
((ComplexAlignFile) source).isShowSeqFeatures());
- ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
- colourSchemeName, al);
+ ColourSchemeI cs = ColourSchemeMapper
+ .getJalviewColourScheme(colourSchemeName, al);
if (cs != null)
{
alignFrame.changeColour(cs);
.applyFeaturesStyle(proxyColourScheme);
}
alignFrame.statusBar.setText(MessageManager.formatMessage(
- "label.successfully_loaded_file",
- new String[] { title }));
+ "label.successfully_loaded_file", new String[]
+ { title }));
if (raiseGUI)
{
try
{
- alignFrame.setMaximum(jalview.bin.Cache.getDefault(
- "SHOW_FULLSCREEN", false));
+ alignFrame.setMaximum(jalview.bin.Cache
+ .getDefault("SHOW_FULLSCREEN", false));
} catch (java.beans.PropertyVetoException ex)
{
}
Desktop.instance.stopLoading();
}
- final String errorMessage = MessageManager
- .getString("label.couldnt_load_file")
- + " "
- + title
- + "\n" + error;
+ final String errorMessage = MessageManager.getString(
+ "label.couldnt_load_file") + " " + title + "\n" + error;
// TODO: refactor FileLoader to be independent of Desktop / Applet GUI
// bits ?
if (raiseGUI && Desktop.desktop != null)
public void run()
{
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- errorMessage, MessageManager
+ errorMessage,
+ MessageManager
.getString("label.error_loading_file"),
JvOptionPane.WARNING_MESSAGE);
}
@Override
public void run()
{
- JvOptionPane.showInternalMessageDialog(
- Desktop.desktop, MessageManager.formatMessage(
- "label.problems_opening_file",
- new String[] { file }), MessageManager
- .getString("label.file_open_error"),
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.problems_opening_file", new String[]
+ { file }),
+ MessageManager.getString("label.file_open_error"),
JvOptionPane.WARNING_MESSAGE);
}
});
@Override
public void run()
{
- JvOptionPane.showInternalMessageDialog(
- Desktop.desktop, MessageManager.formatMessage(
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
"warn.out_of_memory_loading_file", new String[]
- { file }), MessageManager
- .getString("label.out_of_memory"),
+ { file }),
+ MessageManager.getString("label.out_of_memory"),
JvOptionPane.WARNING_MESSAGE);
}
});
String seprator = System.getProperty("file.separator");
String jvTempDir = System.getProperty("java.io.tmpdir") + "jalview"
+ seprator + System.currentTimeMillis();
- File tempStructFile = new File(jvTempDir + seprator + fileName + "."
- + extension);
+ File tempStructFile = new File(
+ jvTempDir + seprator + fileName + "." + extension);
tempStructFile.mkdirs();
return tempStructFile.toString();
}
{
if (from == null)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_null_fileparse"));
+ throw new Error(MessageManager
+ .getString("error.implementation_error_null_fileparse"));
}
if (from == this)
{
private BufferedReader tryAsGzipSource(InputStream inputStream)
throws Exception
{
- BufferedReader inData = new BufferedReader(new InputStreamReader(
- new GZIPInputStream(inputStream)));
+ BufferedReader inData = new BufferedReader(
+ new InputStreamReader(new GZIPInputStream(inputStream)));
inData.mark(2048);
inData.read();
inData.reset();
return inData;
}
- private boolean checkURLSource(String fileStr) throws IOException,
- MalformedURLException
+ private boolean checkURLSource(String fileStr)
+ throws IOException, MalformedURLException
{
errormessage = "URL NOT FOUND";
URL url = new URL(fileStr);
{
if (e != null)
{
- throw new IOException(
- MessageManager
- .getString("exception.failed_to_resolve_gzip_stream"),
- e);
+ throw new IOException(MessageManager
+ .getString("exception.failed_to_resolve_gzip_stream"), e);
}
throw q;
}
{
throw new IOException(MessageManager.formatMessage(
"exception.problem_opening_file_also_tried",
- new String[] { inFile.getName(), suffixLess,
- errormessage }));
+ new String[]
+ { inFile.getName(), suffixLess, errormessage }));
}
}
else
{
throw new IOException(MessageManager.formatMessage(
- "exception.problem_opening_file",
- new String[] { inFile.getName(), errormessage }));
+ "exception.problem_opening_file", new String[]
+ { inFile.getName(), errormessage }));
}
}
}
{
// pass up the reason why we have no source to read from
throw new IOException(MessageManager.formatMessage(
- "exception.failed_to_read_data_from_source",
- new String[] { errormessage }));
+ "exception.failed_to_read_data_from_source", new String[]
+ { errormessage }));
}
error = false;
dataIn.mark(READAHEAD_LIMIT);
{
return dataIn.readLine();
}
- throw new IOException(MessageManager.formatMessage(
- "exception.invalid_source_stream",
- new String[] { errormessage }));
+ throw new IOException(MessageManager
+ .formatMessage("exception.invalid_source_stream", new String[]
+ { errormessage }));
}
/**
}
else
{
- throw new IOException(
- MessageManager
- .getString("error.implementation_error_reset_called_for_invalid_source"));
+ throw new IOException(MessageManager.getString(
+ "error.implementation_error_reset_called_for_invalid_source"));
}
}
startIndex = startEnd[0];
endIndex = startEnd[1];
// get first non-gaped residue start position
- while (Comparison.isGap(seqs[i]
- .getCharAt(startIndex)) && startIndex < endIndex)
+ while (Comparison.isGap(seqs[i].getCharAt(startIndex))
+ && startIndex < endIndex)
{
startIndex++;
}
};
}
AlignmentExportData exportData = jalview.gui.AlignFrame
- .getAlignmentForExport(FileFormat.Json,
- ap.getAlignViewport(), exportSettings);
+ .getAlignmentForExport(FileFormat.Json, ap.getAlignViewport(),
+ exportSettings);
String bioJSON = new FormatAdapter(ap, exportData.getSettings())
.formatSequences(FileFormat.Json, exportData.getAlignment(),
- exportData.getOmitHidden(), exportData
-.getStartEndPostions(), ap.getAlignViewport()
+ exportData.getOmitHidden(),
+ exportData.getStartEndPostions(), ap.getAlignViewport()
.getAlignment().getHiddenColumns());
return bioJSON;
}
{
sb.append(line).append(lineSeparator);
}
-
+
} catch (Exception ex)
{
ex.printStackTrace();
{
isReader.close();
}
-
+
if (buffReader != null)
{
buffReader.close();
public static String getImageMapHTML()
{
- return new String(
- "<html>\n"
- + "<head>\n"
- + "<script language=\"JavaScript\">\n"
- + "var ns4 = document.layers;\n"
- + "var ns6 = document.getElementById && !document.all;\n"
- + "var ie4 = document.all;\n"
- + "offsetX = 0;\n"
- + "offsetY = 20;\n"
- + "var toolTipSTYLE=\"\";\n"
- + "function initToolTips()\n"
- + "{\n"
- + " if(ns4||ns6||ie4)\n"
- + " {\n"
- + " if(ns4) toolTipSTYLE = document.toolTipLayer;\n"
- + " else if(ns6) toolTipSTYLE = document.getElementById(\"toolTipLayer\").style;\n"
- + " else if(ie4) toolTipSTYLE = document.all.toolTipLayer.style;\n"
- + " if(ns4) document.captureEvents(Event.MOUSEMOVE);\n"
- + " else\n"
- + " {\n"
- + " toolTipSTYLE.visibility = \"visible\";\n"
- + " toolTipSTYLE.display = \"none\";\n"
- + " }\n"
- + " document.onmousemove = moveToMouseLoc;\n"
- + " }\n"
- + "}\n"
- + "function toolTip(msg, fg, bg)\n"
- + "{\n"
- + " if(toolTip.arguments.length < 1) // hide\n"
- + " {\n"
- + " if(ns4) toolTipSTYLE.visibility = \"hidden\";\n"
- + " else toolTipSTYLE.display = \"none\";\n"
- + " }\n"
- + " else // show\n"
- + " {\n"
- + " if(!fg) fg = \"#555555\";\n"
- + " if(!bg) bg = \"#FFFFFF\";\n"
- + " var content =\n"
- + " '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + fg + '\"><td>' +\n"
- + " '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + bg + \n"
- + " '\"><td align=\"center\"><font face=\"sans-serif\" color=\"' + fg +\n"
- + " '\" size=\"-2\"> ' + msg +\n"
- + " ' </font></td></table></td></table>';\n"
- + " if(ns4)\n"
- + " {\n"
- + " toolTipSTYLE.document.write(content);\n"
- + " toolTipSTYLE.document.close();\n"
- + " toolTipSTYLE.visibility = \"visible\";\n"
- + " }\n"
- + " if(ns6)\n"
- + " {\n"
- + " document.getElementById(\"toolTipLayer\").innerHTML = content;\n"
- + " toolTipSTYLE.display='block'\n"
- + " }\n"
- + " if(ie4)\n"
- + " {\n"
- + " document.all(\"toolTipLayer\").innerHTML=content;\n"
- + " toolTipSTYLE.display='block'\n"
- + " }\n"
- + " }\n"
- + "}\n"
- + "function moveToMouseLoc(e)\n"
- + "{\n"
- + " if(ns4||ns6)\n"
- + " {\n"
- + " x = e.pageX;\n"
- + " y = e.pageY;\n"
- + " }\n"
- + " else\n"
- + " {\n"
- + " x = event.x + document.body.scrollLeft;\n"
- + " y = event.y + document.body.scrollTop;\n"
- + " }\n"
- + " toolTipSTYLE.left = x + offsetX;\n"
- + " toolTipSTYLE.top = y + offsetY;\n"
- + " return true;\n"
- + "}\n"
- + "</script>\n"
- + "</head>\n"
- + "<body>\n"
- + "<div id=\"toolTipLayer\" style=\"position:absolute; visibility: hidden\"></div>\n"
- + "<script language=\"JavaScript\"><!--\n"
- + "initToolTips(); //--></script>\n");
+ return new String("<html>\n" + "<head>\n"
+ + "<script language=\"JavaScript\">\n"
+ + "var ns4 = document.layers;\n"
+ + "var ns6 = document.getElementById && !document.all;\n"
+ + "var ie4 = document.all;\n" + "offsetX = 0;\n"
+ + "offsetY = 20;\n" + "var toolTipSTYLE=\"\";\n"
+ + "function initToolTips()\n" + "{\n" + " if(ns4||ns6||ie4)\n"
+ + " {\n"
+ + " if(ns4) toolTipSTYLE = document.toolTipLayer;\n"
+ + " else if(ns6) toolTipSTYLE = document.getElementById(\"toolTipLayer\").style;\n"
+ + " else if(ie4) toolTipSTYLE = document.all.toolTipLayer.style;\n"
+ + " if(ns4) document.captureEvents(Event.MOUSEMOVE);\n"
+ + " else\n" + " {\n"
+ + " toolTipSTYLE.visibility = \"visible\";\n"
+ + " toolTipSTYLE.display = \"none\";\n" + " }\n"
+ + " document.onmousemove = moveToMouseLoc;\n" + " }\n"
+ + "}\n" + "function toolTip(msg, fg, bg)\n" + "{\n"
+ + " if(toolTip.arguments.length < 1) // hide\n" + " {\n"
+ + " if(ns4) toolTipSTYLE.visibility = \"hidden\";\n"
+ + " else toolTipSTYLE.display = \"none\";\n" + " }\n"
+ + " else // show\n" + " {\n"
+ + " if(!fg) fg = \"#555555\";\n"
+ + " if(!bg) bg = \"#FFFFFF\";\n" + " var content =\n"
+ + " '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + fg + '\"><td>' +\n"
+ + " '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + bg + \n"
+ + " '\"><td align=\"center\"><font face=\"sans-serif\" color=\"' + fg +\n"
+ + " '\" size=\"-2\"> ' + msg +\n"
+ + " ' </font></td></table></td></table>';\n"
+ + " if(ns4)\n" + " {\n"
+ + " toolTipSTYLE.document.write(content);\n"
+ + " toolTipSTYLE.document.close();\n"
+ + " toolTipSTYLE.visibility = \"visible\";\n" + " }\n"
+ + " if(ns6)\n" + " {\n"
+ + " document.getElementById(\"toolTipLayer\").innerHTML = content;\n"
+ + " toolTipSTYLE.display='block'\n" + " }\n"
+ + " if(ie4)\n" + " {\n"
+ + " document.all(\"toolTipLayer\").innerHTML=content;\n"
+ + " toolTipSTYLE.display='block'\n" + " }\n" + " }\n"
+ + "}\n" + "function moveToMouseLoc(e)\n" + "{\n"
+ + " if(ns4||ns6)\n" + " {\n" + " x = e.pageX;\n"
+ + " y = e.pageY;\n" + " }\n" + " else\n" + " {\n"
+ + " x = event.x + document.body.scrollLeft;\n"
+ + " y = event.y + document.body.scrollTop;\n" + " }\n"
+ + " toolTipSTYLE.left = x + offsetX;\n"
+ + " toolTipSTYLE.top = y + offsetY;\n" + " return true;\n"
+ + "}\n" + "</script>\n" + "</head>\n" + "<body>\n"
+ + "<div id=\"toolTipLayer\" style=\"position:absolute; visibility: hidden\"></div>\n"
+ + "<script language=\"JavaScript\"><!--\n"
+ + "initToolTips(); //--></script>\n");
}
"HTML files");
jvFileChooser.setFileView(new JalviewFileView());
- jvFileChooser.setDialogTitle(MessageManager
- .getString("label.save_as_html"));
+ jvFileChooser
+ .setDialogTitle(MessageManager.getString("label.save_as_html"));
jvFileChooser.setToolTipText(MessageManager.getString("action.save"));
int fileChooserOpt = jvFileChooser.showSaveDialog(null);
if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
{
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", jvFileChooser
- .getSelectedFile().getParent());
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+ jvFileChooser.getSelectedFile().getParent());
selectedFile = jvFileChooser.getSelectedFile().getPath();
}
else
public class HtmlSvgOutput extends HTMLOutput
{
-
public HtmlSvgOutput(AlignmentPanel ap)
{
super(ap);
return;
} catch (Exception e)
{
- setProgressMessage(MessageManager.formatMessage(
- "info.error_creating_file", "HTML"));
+ setProgressMessage(MessageManager
+ .formatMessage("info.error_creating_file", "HTML"));
e.printStackTrace();
return;
}
htmlSvg.append("<html>\n");
if (jsonData != null)
{
- htmlSvg.append("<button onclick=\"javascipt:openJalviewUsingCurrentUrl();\">Launch in Jalview</button> ");
- htmlSvg.append("<input type=\"submit\" value=\"View raw BioJSON Data\" onclick=\"jQuery.facebox({ div:'#seqData' }); return false;\" />");
- htmlSvg.append("<div style=\"display: none;\" name=\"seqData\" id=\"seqData\" >"
- + jsonData + "</div>");
+ htmlSvg.append(
+ "<button onclick=\"javascipt:openJalviewUsingCurrentUrl();\">Launch in Jalview</button> ");
+ htmlSvg.append(
+ "<input type=\"submit\" value=\"View raw BioJSON Data\" onclick=\"jQuery.facebox({ div:'#seqData' }); return false;\" />");
+ htmlSvg.append(
+ "<div style=\"display: none;\" name=\"seqData\" id=\"seqData\" >"
+ + jsonData + "</div>");
htmlSvg.append("<br/> ");
}
htmlSvg.append("\n<style type=\"text/css\"> "
if (jsonData != null)
{
// facebox style sheet for displaying raw BioJSON data
- htmlSvg.append("#facebox { position: absolute; top: 0; left: 0; z-index: 100; text-align: left; }\n"
- + "#facebox .popup{ position:relative; border:3px solid rgba(0,0,0,0); -webkit-border-radius:5px;"
- + "-moz-border-radius:5px; border-radius:5px; -webkit-box-shadow:0 0 18px rgba(0,0,0,0.4); -moz-box-shadow:0 0 18px rgba(0,0,0,0.4);"
- + "box-shadow:0 0 18px rgba(0,0,0,0.4); }\n"
- + "#facebox .content { display:table; width: 98%; padding: 10px; background: #fff; -webkit-border-radius:4px; -moz-border-radius:4px;"
- + " border-radius:4px; }\n"
- + "#facebox .content > p:first-child{ margin-top:0; }\n"
- + "#facebox .content > p:last-child{ margin-bottom:0; }\n"
- + "#facebox .close{ position:absolute; top:5px; right:5px; padding:2px; background:#fff; }\n"
- + "#facebox .close img{ opacity:0.3; }\n"
- + "#facebox .close:hover img{ opacity:1.0; }\n"
- + "#facebox .loading { text-align: center; }\n"
- + "#facebox .image { text-align: center;}\n"
- + "#facebox img { border: 0; margin: 0; }\n"
- + "#facebox_overlay { position: fixed; top: 0px; left: 0px; height:100%; width:100%; }\n"
- + ".facebox_hide { z-index:-100; }\n"
- + ".facebox_overlayBG { background-color: #000; z-index: 99; }");
+ htmlSvg.append(
+ "#facebox { position: absolute; top: 0; left: 0; z-index: 100; text-align: left; }\n"
+ + "#facebox .popup{ position:relative; border:3px solid rgba(0,0,0,0); -webkit-border-radius:5px;"
+ + "-moz-border-radius:5px; border-radius:5px; -webkit-box-shadow:0 0 18px rgba(0,0,0,0.4); -moz-box-shadow:0 0 18px rgba(0,0,0,0.4);"
+ + "box-shadow:0 0 18px rgba(0,0,0,0.4); }\n"
+ + "#facebox .content { display:table; width: 98%; padding: 10px; background: #fff; -webkit-border-radius:4px; -moz-border-radius:4px;"
+ + " border-radius:4px; }\n"
+ + "#facebox .content > p:first-child{ margin-top:0; }\n"
+ + "#facebox .content > p:last-child{ margin-bottom:0; }\n"
+ + "#facebox .close{ position:absolute; top:5px; right:5px; padding:2px; background:#fff; }\n"
+ + "#facebox .close img{ opacity:0.3; }\n"
+ + "#facebox .close:hover img{ opacity:1.0; }\n"
+ + "#facebox .loading { text-align: center; }\n"
+ + "#facebox .image { text-align: center;}\n"
+ + "#facebox img { border: 0; margin: 0; }\n"
+ + "#facebox_overlay { position: fixed; top: 0px; left: 0px; height:100%; width:100%; }\n"
+ + ".facebox_hide { z-index:-100; }\n"
+ + ".facebox_overlayBG { background-color: #000; z-index: 99; }");
}
htmlSvg.append("</style>");
if (!wrapped)
{
- htmlSvg.append("<div class=\"main-container\" \n>");
- htmlSvg.append("<div class=\"titlex\">\n");
- htmlSvg.append("<div class=\"sub-category-container\"> \n");
- htmlSvg.append(titleSvg);
- htmlSvg.append("</div>");
- htmlSvg.append("</div>\n\n<!-- ========================================================================================== -->\n\n");
- htmlSvg.append("<div class=\"align\" >");
- htmlSvg.append(
- "<div class=\"sub-category-container\"> <div style=\"overflow-x: scroll;\">")
- .append(alignmentSvg).append("</div></div>").append("</div>");
- htmlSvg.append("</div>");
+ htmlSvg.append("<div class=\"main-container\" \n>");
+ htmlSvg.append("<div class=\"titlex\">\n");
+ htmlSvg.append("<div class=\"sub-category-container\"> \n");
+ htmlSvg.append(titleSvg);
+ htmlSvg.append("</div>");
+ htmlSvg.append(
+ "</div>\n\n<!-- ========================================================================================== -->\n\n");
+ htmlSvg.append("<div class=\"align\" >");
+ htmlSvg.append(
+ "<div class=\"sub-category-container\"> <div style=\"overflow-x: scroll;\">")
+ .append(alignmentSvg).append("</div></div>").append("</div>");
+ htmlSvg.append("</div>");
- htmlSvg.append("<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://ajax.googleapis.com/ajax/libs/jquery/1/jquery.min.js\"></script>\n"
- + "<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://ajax.googleapis.com/ajax/libs/jqueryui/1.11.2/jquery-ui.min.js\"></script>\n"
- + "<script>\n"
- + "var subCatContainer = $(\".sub-category-container\");\n"
- + "subCatContainer.scroll(\nfunction() {\n"
- + "subCatContainer.scrollTop($(this).scrollTop());\n});\n");
+ htmlSvg.append(
+ "<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://ajax.googleapis.com/ajax/libs/jquery/1/jquery.min.js\"></script>\n"
+ + "<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://ajax.googleapis.com/ajax/libs/jqueryui/1.11.2/jquery-ui.min.js\"></script>\n"
+ + "<script>\n"
+ + "var subCatContainer = $(\".sub-category-container\");\n"
+ + "subCatContainer.scroll(\nfunction() {\n"
+ + "subCatContainer.scrollTop($(this).scrollTop());\n});\n");
- htmlSvg.append("</script>\n");
+ htmlSvg.append("</script>\n");
}
else
{
- htmlSvg.append("<div>\n")
- .append(alignmentSvg).append("</div>");
- htmlSvg.append("<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://ajax.googleapis.com/ajax/libs/jquery/1/jquery.min.js\"></script>\n"
- + "<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://ajax.googleapis.com/ajax/libs/jqueryui/1.11.2/jquery-ui.min.js\"></script>\n");
+ htmlSvg.append("<div>\n").append(alignmentSvg).append("</div>");
+ htmlSvg.append(
+ "<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://ajax.googleapis.com/ajax/libs/jquery/1/jquery.min.js\"></script>\n"
+ + "<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://ajax.googleapis.com/ajax/libs/jqueryui/1.11.2/jquery-ui.min.js\"></script>\n");
}
// javascript for launching file in Jalview
htmlSvg.append("<script language=\"JavaScript\">\n");
htmlSvg.append("function openJalviewUsingCurrentUrl(){\n");
- htmlSvg.append(" var json = JSON.parse(document.getElementById(\"seqData\").innerHTML);\n");
- htmlSvg.append(" var jalviewVersion = json['appSettings'].version;\n");
+ htmlSvg.append(
+ " var json = JSON.parse(document.getElementById(\"seqData\").innerHTML);\n");
+ htmlSvg.append(
+ " var jalviewVersion = json['appSettings'].version;\n");
htmlSvg.append(" var url = json['appSettings'].webStartUrl;\n");
- htmlSvg.append(" var myForm = document.createElement(\"form\");\n\n");
+ htmlSvg.append(
+ " var myForm = document.createElement(\"form\");\n\n");
htmlSvg.append(" var heap = document.createElement(\"input\");\n");
htmlSvg.append(" heap.setAttribute(\"name\", \"jvm-max-heap\") ;\n");
htmlSvg.append(" heap.setAttribute(\"value\", \"2G\");\n\n");
htmlSvg.append(" var target = document.createElement(\"input\");\n");
htmlSvg.append(" target.setAttribute(\"name\", \"open\");\n");
htmlSvg.append(" target.setAttribute(\"value\", document.URL);\n\n");
- htmlSvg.append(" var jvVersion = document.createElement(\"input\");\n");
+ htmlSvg.append(
+ " var jvVersion = document.createElement(\"input\");\n");
htmlSvg.append(" jvVersion.setAttribute(\"name\", \"version\") ;\n");
- htmlSvg.append(" jvVersion.setAttribute(\"value\", jalviewVersion);\n\n");
+ htmlSvg.append(
+ " jvVersion.setAttribute(\"value\", jalviewVersion);\n\n");
htmlSvg.append(" myForm.action = url;\n");
htmlSvg.append(" myForm.appendChild(heap);\n");
htmlSvg.append(" myForm.appendChild(target);\n");
@Override
public boolean isEmbedData()
{
- return Boolean.valueOf(jalview.bin.Cache.getDefault(
- "EXPORT_EMBBED_BIOJSON", "true"));
+ return Boolean.valueOf(
+ jalview.bin.Cache.getDefault("EXPORT_EMBBED_BIOJSON", "true"));
}
@Override
String idPanelSvgData = idPanelGraphics.getSVGDocument();
String alignPanelSvgData = alignPanelGraphics.getSVGDocument();
String jsonData = getBioJSONData();
- String htmlData = getHtml(idPanelSvgData, alignPanelSvgData,
- jsonData, ap.av.getWrapAlignment());
+ String htmlData = getHtml(idPanelSvgData, alignPanelSvgData, jsonData,
+ ap.av.getWrapAlignment());
FileOutputStream out = new FileOutputStream(generatedFile);
out.write(htmlData.getBytes());
out.flush();
out.close();
- setProgressMessage(MessageManager.formatMessage(
- "status.export_complete", "HTML"));
+ setProgressMessage(MessageManager
+ .formatMessage("status.export_complete", "HTML"));
exportCompleted();
} catch (OutOfMemoryError err)
{
} catch (Exception e)
{
e.printStackTrace();
- setProgressMessage(MessageManager.formatMessage(
- "info.error_creating_file", "HTML"));
+ setProgressMessage(MessageManager
+ .formatMessage("info.error_creating_file", "HTML"));
}
}
}
// preserves original behaviour prior to version 2.3
}
- public FileFormatI identify(AlignmentFileReaderI file, boolean closeSource)
- throws IOException
+ public FileFormatI identify(AlignmentFileReaderI file,
+ boolean closeSource) throws IOException
{
- FileParse fp = new FileParse(file.getInFile(), file.getDataSourceType());
+ FileParse fp = new FileParse(file.getInFile(),
+ file.getDataSourceType());
return identify(fp, closeSource);
}
break;
}
- if ((data.indexOf("//") == 0)
- || ((data.indexOf("!!") > -1) && (data.indexOf("!!") < data
- .indexOf("_MULTIPLE_ALIGNMENT "))))
+ if ((data.indexOf("//") == 0) || ((data.indexOf("!!") > -1) && (data
+ .indexOf("!!") < data.indexOf("_MULTIPLE_ALIGNMENT "))))
{
reply = FileFormat.MSF;
}
if (trimmedLength == 0)
{
- System.err
- .println("File Identification failed! - Empty file was read.");
+ System.err.println(
+ "File Identification failed! - Empty file was read.");
throw new FileFormatException("EMPTY DATA FILE");
}
System.out.println("File format identified as " + reply.toString());
type = ider.identify(args[i], DataSourceType.FILE);
} catch (FileFormatException e)
{
- System.err.println(String.format(
- "Error '%s' identifying file type for %s", args[i],
- e.getMessage()));
+ System.err.println(
+ String.format("Error '%s' identifying file type for %s",
+ args[i], e.getMessage()));
}
System.out.println("Type of " + args[i] + " is " + type);
}
for (int j = 0; j < i; j++)
{
- scores.setElementAt(
- ((Float) scores.elementAt(j)).toString(), j);
+ scores.setElementAt(((Float) scores.elementAt(j)).toString(),
+ j);
}
scores.addElement(ascore);
{
// Add all sequence like objects
Sequence newSeq = new Sequence(ids.elementAt(i).toString(),
- seq_entries.elementAt(i).toString(), 1, seq_entries
- .elementAt(i).toString().length());
+ seq_entries.elementAt(i).toString(), 1,
+ seq_entries.elementAt(i).toString().length());
if (maxLength != seq_entries.elementAt(i).toString().length())
{
- throw new IOException(
- MessageManager
- .formatMessage(
- "exception.jpredconcide_entry_has_unexpected_number_of_columns",
- new String[] { ids.elementAt(i).toString() }));
+ throw new IOException(MessageManager.formatMessage(
+ "exception.jpredconcide_entry_has_unexpected_number_of_columns",
+ new String[]
+ { ids.elementAt(i).toString() }));
}
- if ((newSeq.getName().startsWith("QUERY") || newSeq.getName()
- .startsWith("align;")) && (QuerySeqPosition == -1))
+ if ((newSeq.getName().startsWith("QUERY")
+ || newSeq.getName().startsWith("align;"))
+ && (QuerySeqPosition == -1))
{
QuerySeqPosition = seqs.size();
}
} catch (Exception e)
{
tal = null;
- IOException ex = new IOException(
- MessageManager
- .formatMessage(
- "exception.couldnt_parse_concise_annotation_for_prediction",
- new String[] { e.getMessage() }));
+ IOException ex = new IOException(MessageManager.formatMessage(
+ "exception.couldnt_parse_concise_annotation_for_prediction",
+ new String[]
+ { e.getMessage() }));
e.printStackTrace(); // java 1.1 does not have :
// ex.setStackTrace(e.getStackTrace());
throw ex;
// are not exported
if (globalColourScheme
.equalsIgnoreCase(JalviewColourScheme.RNAHelices.toString())
- || globalColourScheme
- .equalsIgnoreCase(JalviewColourScheme.TCoffee
- .toString()))
+ || globalColourScheme.equalsIgnoreCase(
+ JalviewColourScheme.TCoffee.toString()))
{
jsonAlignmentPojo.setGlobalColorScheme(ResidueColourScheme.NONE);
}
SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
String.valueOf(seq.hashCode()));
- String featureColour = (fr == null) ? null : jalview.util.Format
- .getHexString(finder.findFeatureColour(Color.white, seq,
- seq.findIndex(sf.getBegin())));
+ String featureColour = (fr == null) ? null
+ : jalview.util.Format.getHexString(
+ finder.findFeatureColour(Color.white, seq,
+ seq.findIndex(sf.getBegin())));
jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
jsonFeature.setXend(seq.findIndex(sf.getEnd()));
jsonFeature.setType(sf.getType());
annotationPojo.setDisplayCharacter(displayChar);
if (annotation.colour != null)
{
- annotationPojo.setColour(jalview.util.Format
- .getHexString(annotation.colour));
+ annotationPojo.setColour(
+ jalview.util.Format.getHexString(annotation.colour));
}
alignAnnotPojo.getAnnotations().add(annotationPojo);
}
{
globalColourScheme = (String) jvSettingsJsonObj
.get("globalColorScheme");
- Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
- "showSeqFeatures").toString());
+ Boolean showFeatures = Boolean.valueOf(
+ jvSettingsJsonObj.get("showSeqFeatures").toString());
setShowSeqFeatures(showFeatures);
parseHiddenSeqRefsAsList(jvSettingsJsonObj);
parseHiddenCols(jvSettingsJsonObj);
hiddenSequences = new ArrayList<>();
seqMap = new Hashtable<>();
- for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
- .hasNext();)
+ for (Iterator<JSONObject> sequenceIter = seqJsonArray
+ .iterator(); sequenceIter.hasNext();)
{
JSONObject sequence = sequenceIter.next();
String sequcenceString = sequence.get("seq").toString();
parseFeatures(jsonSeqArray);
- for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
- .hasNext();)
+ for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray
+ .iterator(); seqGrpIter.hasNext();)
{
JSONObject seqGrpObj = seqGrpIter.next();
String grpName = seqGrpObj.get("groupName").toString();
String colourScheme = seqGrpObj.get("colourScheme").toString();
String description = (seqGrpObj.get("description") == null) ? null
: seqGrpObj.get("description").toString();
- boolean displayBoxes = Boolean.valueOf(seqGrpObj
- .get("displayBoxes").toString());
- boolean displayText = Boolean.valueOf(seqGrpObj.get("displayText")
- .toString());
- boolean colourText = Boolean.valueOf(seqGrpObj.get("colourText")
- .toString());
- boolean showNonconserved = Boolean.valueOf(seqGrpObj.get(
- "showNonconserved").toString());
+ boolean displayBoxes = Boolean
+ .valueOf(seqGrpObj.get("displayBoxes").toString());
+ boolean displayText = Boolean
+ .valueOf(seqGrpObj.get("displayText").toString());
+ boolean colourText = Boolean
+ .valueOf(seqGrpObj.get("colourText").toString());
+ boolean showNonconserved = Boolean
+ .valueOf(seqGrpObj.get("showNonconserved").toString());
int startRes = Integer
.valueOf(seqGrpObj.get("startRes").toString());
int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
}
SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
displayBoxes, displayText, colourText, startRes, endRes);
- seqGrp.setColourScheme(ColourSchemeMapper.getJalviewColourScheme(
- colourScheme, seqGrp));
+ seqGrp.setColourScheme(ColourSchemeMapper
+ .getJalviewColourScheme(colourScheme, seqGrp));
seqGrp.setShowNonconserved(showNonconserved);
seqGrp.setDescription(description);
this.seqGroups.add(seqGrp);
}
- for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter
- .hasNext();)
+ for (Iterator<JSONObject> alAnnotIter = alAnnotJsonArray
+ .iterator(); alAnnotIter.hasNext();)
{
JSONObject alAnnot = alAnnotIter.next();
JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
Annotation[] annotations = new Annotation[annotJsonArray.size()];
int count = 0;
- for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
- .hasNext();)
+ for (Iterator<JSONObject> annotIter = annotJsonArray
+ .iterator(); annotIter.hasNext();)
{
JSONObject annot = annotIter.next();
if (annot == null)
}
else
{
- float val = annot.get("value") == null ? null : Float
- .valueOf(annot.get("value").toString());
- String desc = annot.get("description") == null ? null : annot
- .get("description").toString();
+ float val = annot.get("value") == null ? null
+ : Float.valueOf(annot.get("value").toString());
+ String desc = annot.get("description") == null ? null
+ : annot.get("description").toString();
char ss = annot.get("secondaryStructure") == null
|| annot.get("secondaryStructure").toString()
- .equalsIgnoreCase("u0000") ? ' ' : annot
- .get("secondaryStructure").toString().charAt(0);
+ .equalsIgnoreCase("u0000") ? ' '
+ : annot.get("secondaryStructure")
+ .toString().charAt(0);
String displayChar = annot.get("displayCharacter") == null ? ""
: annot.get("displayCharacter").toString();
annotations[count] = new Annotation(displayChar, desc, ss, val);
if (annot.get("colour") != null)
{
- Color color = ColorUtils.parseColourString(annot.get(
- "colour").toString());
+ Color color = ColorUtils
+ .parseColourString(annot.get("colour").toString());
annotations[count].colour = color;
}
}
++count;
}
- AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
- .get("label").toString(), alAnnot.get("description")
- .toString(), annotations);
- alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0 : Integer
- .valueOf(alAnnot.get("graphType").toString());
+ AlignmentAnnotation alignAnnot = new AlignmentAnnotation(
+ alAnnot.get("label").toString(),
+ alAnnot.get("description").toString(), annotations);
+ alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0
+ : Integer.valueOf(alAnnot.get("graphType").toString());
JSONObject diplaySettings = (JSONObject) alAnnot
.get("annotationSettings");
if (diplaySettings != null)
{
- alignAnnot.scaleColLabel = (diplaySettings.get("scaleColLabel") == null) ? false
- : Boolean.valueOf(diplaySettings.get("scaleColLabel")
- .toString());
+ alignAnnot.scaleColLabel = (diplaySettings
+ .get("scaleColLabel") == null) ? false
+ : Boolean.valueOf(diplaySettings
+ .get("scaleColLabel").toString());
alignAnnot.showAllColLabels = (diplaySettings
- .get("showAllColLabels") == null) ? true : Boolean
- .valueOf(diplaySettings.get("showAllColLabels")
- .toString());
+ .get("showAllColLabels") == null) ? true
+ : Boolean.valueOf(diplaySettings
+ .get("showAllColLabels").toString());
alignAnnot.centreColLabels = (diplaySettings
.get("centreColLabels") == null) ? true
- : Boolean.valueOf(diplaySettings.get("centreColLabels")
- .toString());
- alignAnnot.belowAlignment = (diplaySettings.get("belowAlignment") == null) ? false
- : Boolean.valueOf(diplaySettings.get("belowAlignment")
- .toString());
- alignAnnot.visible = (diplaySettings.get("visible") == null) ? true
- : Boolean.valueOf(diplaySettings.get("visible")
- .toString());
- alignAnnot.hasIcons = (diplaySettings.get("hasIcon") == null) ? true
- : Boolean.valueOf(diplaySettings.get("hasIcon")
- .toString());
+ : Boolean.valueOf(diplaySettings
+ .get("centreColLabels").toString());
+ alignAnnot.belowAlignment = (diplaySettings
+ .get("belowAlignment") == null) ? false
+ : Boolean.valueOf(diplaySettings
+ .get("belowAlignment").toString());
+ alignAnnot.visible = (diplaySettings.get("visible") == null)
+ ? true
+ : Boolean.valueOf(
+ diplaySettings.get("visible").toString());
+ alignAnnot.hasIcons = (diplaySettings.get("hasIcon") == null)
+ ? true
+ : Boolean.valueOf(
+ diplaySettings.get("hasIcon").toString());
}
if (alAnnot.get("score") != null)
.valueOf(alAnnot.get("score").toString());
}
- String calcId = (alAnnot.get("calcId") == null) ? "" : alAnnot.get(
- "calcId").toString();
+ String calcId = (alAnnot.get("calcId") == null) ? ""
+ : alAnnot.get("calcId").toString();
alignAnnot.setCalcId(calcId);
- String seqHash = (alAnnot.get("sequenceRef") != null) ? alAnnot
- .get("sequenceRef").toString() : null;
+ String seqHash = (alAnnot.get("sequenceRef") != null)
+ ? alAnnot.get("sequenceRef").toString()
+ : null;
Sequence sequence = (seqHash != null) ? seqMap.get(seqHash) : null;
if (sequence != null)
if (jsonSeqFeatures != null)
{
displayedFeatures = new FeaturesDisplayed();
- for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures.iterator(); seqFeatureItr
- .hasNext();)
+ for (Iterator<JSONObject> seqFeatureItr = jsonSeqFeatures
+ .iterator(); seqFeatureItr.hasNext();)
{
JSONObject jsonFeature = seqFeatureItr.next();
Long begin = (Long) jsonFeature.get("xStart");
}
}
}
- globalColourScheme = ColourSchemeProperty.getColourName(viewport
- .getGlobalColourScheme());
+ globalColourScheme = ColourSchemeProperty
+ .getColourName(viewport.getGlobalColourScheme());
setDisplayedFeatures(viewport.getFeaturesDisplayed());
showSeqFeatures = viewport.isShowSequenceFeatures();
* @param selected
* @return
*/
- public static JalviewFileChooser forRead(String directory, String selected)
+ public static JalviewFileChooser forRead(String directory,
+ String selected)
{
List<String> extensions = new ArrayList<String>();
List<String> descs = new ArrayList<String>();
public JalviewFileChooser(String extension, String desc)
{
this(Cache.getProperty("LAST_DIRECTORY"), new String[] { extension },
- new String[] { desc }, desc, true);
+ new String[]
+ { desc }, desc, true);
}
JalviewFileChooser(String dir, String[] extensions, String[] descs,
}
});
- this.setBorder(new javax.swing.border.TitledBorder(MessageManager
- .getString("label.recently_opened")));
+ this.setBorder(new javax.swing.border.TitledBorder(
+ MessageManager.getString("label.recently_opened")));
final JScrollPane scroller = new JScrollPane(list);
@Override
public void run()
{
- scroller.getHorizontalScrollBar().setValue(
- scroller.getHorizontalScrollBar().getMaximum());
+ scroller.getHorizontalScrollBar()
+ .setValue(scroller.getHorizontalScrollBar().getMaximum());
}
});
String exts = ff.getExtensions();
for (String ext : exts.split(","))
{
- extensions.put(ext.trim().toLowerCase(), desc
- + ("jar".equals(ext) ? " (old)" : ""));
+ extensions.put(ext.trim().toLowerCase(),
+ desc + ("jar".equals(ext) ? " (old)" : ""));
}
}
}
}
else
{
- System.err
- .println("JalviewFileView.createImageIcon: Couldn't find file: "
+ System.err.println(
+ "JalviewFileView.createImageIcon: Couldn't find file: "
+ filePath);
}
icons.put(filePath, icon);
if ((delMap != null && delMap.length > width)
|| (delMap == null && gapmap.length != width))
{
- throw (new Exception(
- MessageManager
- .formatMessage(
- "exception.number_of_residues_in_query_sequence_differ_from_prediction",
- new String[] {
- (delMap == null ? "" : MessageManager
- .getString("label.mapped")),
- al.getSequenceAt(firstSeq).getName(),
- al.getSequenceAt(firstSeq)
- .getSequenceAsString(),
- Integer.valueOf(width).toString() })));
+ throw (new Exception(MessageManager.formatMessage(
+ "exception.number_of_residues_in_query_sequence_differ_from_prediction",
+ new String[]
+ { (delMap == null ? ""
+ : MessageManager.getString("label.mapped")),
+ al.getSequenceAt(firstSeq).getName(),
+ al.getSequenceAt(firstSeq).getSequenceAsString(),
+ Integer.valueOf(width).toString() })));
}
AlignmentAnnotation annot;
{
if (id.startsWith("JNETSOL"))
{
- float amnt = (id.endsWith("25") ? 3f : id.endsWith("5") ? 6f : 9f);
+ float amnt = (id.endsWith("25") ? 3f
+ : id.endsWith("5") ? 6f : 9f);
for (int spos = 0; spos < width; spos++)
{
int sposw = (delMap == null) ? gapmap[spos]
if (!firstsol)
{
// add the solvent accessibility
- annot = new AlignmentAnnotation(
- "Jnet Burial",
+ annot = new AlignmentAnnotation("Jnet Burial",
"<html>Prediction of Solvent Accessibility<br/>levels are<ul><li>0 - Exposed</li><li>3 - 25% or more S.A. accessible</li><li>6 - 5% or more S.A. accessible</li><li>9 - Buried (<5% exposed)</li></ul>",
sol, 0f, 9f, AlignmentAnnotation.BAR_GRAPH);
seqRef.addAlignmentAnnotation(annot);
}
al.addAnnotation(annot);
- al.setAnnotationIndex(annot, al.getAlignmentAnnotation().length
- - existingAnnotations - 1);
+ al.setAnnotationIndex(annot,
+ al.getAlignmentAnnotation().length - existingAnnotations - 1);
}
// Hashtable scores = prediction.getScores();
i++;
}
- Format maxLenpad = new Format("%" + (new String("" + max)).length()
- + "d");
- Format maxChkpad = new Format("%" + (new String("1" + max)).length()
- + "d");
+ Format maxLenpad = new Format(
+ "%" + (new String("" + max)).length() + "d");
+ Format maxChkpad = new Format(
+ "%" + (new String("1" + max)).length() + "d");
i = 0;
int bigChecksum = 0;
*/
final int Types[] = { 0, 0, 1, 0, 1, 0, 0, 0, 0, 0 };
- final char Padding[] = { ' ', ' ', ' ', '.', ' ', '.', '.', '.', '.', '.' };
+ final char Padding[] = { ' ', ' ', ' ', '.', ' ', '.', '.', '.', '.',
+ '.' };
java.util.Hashtable fields = new java.util.Hashtable();
{
// Set start and end before we update the type (in the case of a
// synthesized field set)
- if (getStartCode() == null
- || (getStartNum() != seq.getStart() && getStartCode().val != null))
+ if (getStartCode() == null || (getStartNum() != seq.getStart()
+ && getStartCode().val != null))
{
// unset or user updated sequence start position
setStartCode(seq.getStart());
}
- if (getEndCode() == null
- || (getEndNum() != seq.getEnd() && getStartCode() != null && getStartCode().val != null))
+ if (getEndCode() == null || (getEndNum() != seq.getEnd()
+ && getStartCode() != null && getStartCode().val != null))
{
setEndCode(seq.getEnd());
}
boolean printRootInfo = true;
- private com.stevesoft.pat.Regex[] NodeSafeName = new com.stevesoft.pat.Regex[]
- { new com.stevesoft.pat.Regex().perlCode("m/[\\[,:'()]/"), // test for
+ private com.stevesoft.pat.Regex[] NodeSafeName = new com.stevesoft.pat.Regex[] {
+ new com.stevesoft.pat.Regex().perlCode("m/[\\[,:'()]/"), // test for
// requiring
// quotes
new com.stevesoft.pat.Regex().perlCode("s/'/''/"), // escaping quote
// characters
new com.stevesoft.pat.Regex().perlCode("s/\\/w/_/") // unqoted whitespace
- // transformation
+ // transformation
};
char QuoteChar = '\'';
private String ErrorStringrange(String Error, String Er, int r, int p,
String s)
{
- return ((Error == null) ? "" : Error)
- + Er
- + " at position "
- + p
- + " ( "
+ return ((Error == null) ? "" : Error) + Er + " at position " + p + " ( "
+ s.substring(((p - r) < 0) ? 0 : (p - r),
- ((p + r) > s.length()) ? s.length() : (p + r)) + " )\n";
+ ((p + r) > s.length()) ? s.length() : (p + r))
+ + " )\n";
}
// @tree annotations
if (qnodename.searchFrom(nf, fcp))
{
int nl = qnodename.stringMatched().length();
- nodename = new String(qnodename.stringMatched().substring(1,
- nl - 1));
+ nodename = new String(
+ qnodename.stringMatched().substring(1, nl - 1));
// unpack any escaped colons
com.stevesoft.pat.Regex xpandquotes = com.stevesoft.pat.Regex
.perlCode("s/''/'/");
{
if (d != -1)
{
- Error = ErrorStringrange(Error, "Wayward semicolon (depth=" + d
- + ")", 7, fcp, nf);
+ Error = ErrorStringrange(Error,
+ "Wayward semicolon (depth=" + d + ")", 7, fcp, nf);
}
// cp advanced at the end of default
}
* '"+nf.substring(cp,fcp)+"'"); }
*/
// verify termination.
- com.stevesoft.pat.Regex comment = new com.stevesoft.pat.Regex("]");
+ com.stevesoft.pat.Regex comment = new com.stevesoft.pat.Regex(
+ "]");
if (comment.searchFrom(nf, fcp))
{
// Skip the comment field
com.stevesoft.pat.Regex ndist = new com.stevesoft.pat.Regex(
":([-0-9Ee.+]+)");
- if (!parsednodename
- && uqnodename.search(fstring)
+ if (!parsednodename && uqnodename.search(fstring)
&& ((uqnodename.matchedFrom(1) == 0) || (fstring
.charAt(uqnodename.matchedFrom(1) - 1) != ':'))) // JBPNote
// HACK!
if (nbootstrap.search(fstring))
{
- if (nbootstrap.stringMatched(1).equals(
- uqnodename.stringMatched(1)))
+ if (nbootstrap.stringMatched(1)
+ .equals(uqnodename.stringMatched(1)))
{
nodename = null; // no nodename here.
}
- if (nodename == null
- || nodename.length() == 0
- || nbootstrap.matchedFrom(1) > (uqnodename.matchedFrom(1) + uqnodename
- .stringMatched().length()))
+ if (nodename == null || nodename.length() == 0
+ || nbootstrap.matchedFrom(1) > (uqnodename.matchedFrom(1)
+ + uqnodename.stringMatched().length()))
{
try
{
HasBootstrap = true;
} catch (Exception e)
{
- Error = ErrorStringrange(Error,
- "Can't parse bootstrap value", 4,
- ncp + nbootstrap.matchedFrom(), nf);
+ Error = ErrorStringrange(Error, "Can't parse bootstrap value",
+ 4, ncp + nbootstrap.matchedFrom(), nf);
}
}
}
if ((d > -1) && (c == null))
{
- Error = ErrorStringrange(
- Error,
+ Error = ErrorStringrange(Error,
"File broke algorithm: Lost place in tree (is there an extra ')' ?)",
7, fcp, nf);
}
if (Error != null)
{
- throw (new IOException(MessageManager.formatMessage(
- "exception.newfile", new String[] { Error.toString() })));
+ throw (new IOException(
+ MessageManager.formatMessage("exception.newfile", new String[]
+ { Error.toString() })));
}
if (root == null)
{
- throw (new IOException(MessageManager.formatMessage(
- "exception.newfile", new String[] { MessageManager
- .getString("label.no_tree_read_in") })));
+ throw (new IOException(
+ MessageManager.formatMessage("exception.newfile", new String[]
+ { MessageManager.getString("label.no_tree_read_in") })));
}
// THe next line is failing for topali trees - not sure why yet. if
// (root.right()!=null && root.isDummy())
// more codes here.
} catch (Exception e)
{
- System.err.println("Couldn't parse code '" + code + "' = '"
- + value + "'");
+ System.err.println(
+ "Couldn't parse code '" + code + "' = '" + value + "'");
e.printStackTrace(System.err);
}
}
private String printNodeField(SequenceNode c)
{
return ((c.getName() == null) ? "" : nodeName(c.getName()))
- + ((HasBootstrap) ? ((c.getBootstrap() > -1) ? ((c.getName() != null ? " "
- : "") + c.getBootstrap())
- : "")
- : "") + ((HasDistances) ? (":" + c.dist) : "");
+ + ((HasBootstrap) ? ((c.getBootstrap() > -1)
+ ? ((c.getName() != null ? " " : "") + c.getBootstrap())
+ : "") : "")
+ + ((HasDistances) ? (":" + c.dist) : "");
}
/**
*/
private String printRootField(SequenceNode root)
{
- return (printRootInfo) ? (((root.getName() == null) ? ""
- : nodeName(root.getName()))
- + ((HasBootstrap) ? ((root.getBootstrap() > -1) ? ((root
- .getName() != null ? " " : "") + +root.getBootstrap())
- : "") : "") + ((RootHasDistance) ? (":" + root.dist)
- : "")) : "";
+ return (printRootInfo)
+ ? (((root.getName() == null) ? "" : nodeName(root.getName()))
+ + ((HasBootstrap)
+ ? ((root.getBootstrap() > -1)
+ ? ((root.getName() != null ? " " : "")
+ + +root.getBootstrap())
+ : "")
+ : "")
+ + ((RootHasDistance) ? (":" + root.dist) : ""))
+ : "";
}
// Non recursive call deals with root node properties
{
if (args == null || args.length != 1)
{
- System.err
- .println("Takes one argument - file name of a newick tree file.");
+ System.err.println(
+ "Takes one argument - file name of a newick tree file.");
System.exit(0);
}
if (noSeqs < 1)
{
- throw new IOException(
- MessageManager.getString("exception.pfam_no_sequences_found"));
+ throw new IOException(MessageManager
+ .getString("exception.pfam_no_sequences_found"));
}
for (i = 0; i < headers.size(); i++)
}
Sequence newSeq = parseId(headers.get(i).toString());
- newSeq.setSequence(seqhash.get(headers.get(i).toString())
- .toString());
+ newSeq.setSequence(
+ seqhash.get(headers.get(i).toString()).toString());
seqs.addElement(newSeq);
}
else
/**
* <p>
- * Parser and exporter for PHYLIP file format, as defined <a
- * href="http://evolution.genetics.washington.edu/phylip/doc/main.html">in the
- * documentation</a>. The parser imports PHYLIP files in both sequential and
+ * Parser and exporter for PHYLIP file format, as defined
+ * <a href="http://evolution.genetics.washington.edu/phylip/doc/main.html">in
+ * the documentation</a>. The parser imports PHYLIP files in both sequential and
* interleaved format, and (currently) exports in interleaved format (using 60
* characters per matrix for the sequence).
* <p>
* The following assumptions have been made for input
* <ul>
* <li>Sequences are expressed as letters, not real numbers with decimal points
- * separated by blanks (which is a valid option according to the specification)</li>
+ * separated by blanks (which is a valid option according to the
+ * specification)</li>
* </ul>
*
* The following assumptions have been made for output
"First line must contain the number of specifies and number of characters");
}
- int numberSpecies = Integer.parseInt(lineElements[0]), numberCharacters = Integer
- .parseInt(lineElements[1]);
+ int numberSpecies = Integer.parseInt(lineElements[0]),
+ numberCharacters = Integer.parseInt(lineElements[1]);
if (numberSpecies <= 0)
{
}
else
{
- sequenceElements[i] = parseId(validateName(potentialName
- .substring(0, tabIndex)));
+ sequenceElements[i] = parseId(
+ validateName(potentialName.substring(0, tabIndex)));
sequences[i] = new StringBuffer(
removeWhitespace(line.substring(tabIndex)));
}
{
if (name.indexOf(c) > -1)
{
- throw new IOException("Species name contains illegal character "
- + c);
+ throw new IOException(
+ "Species name contains illegal character " + c);
}
}
return name;
int start = i * numInterleavedColumns;
for (SequenceI s : sqs)
{
- sb.append(
- s.getSequence(start, Math.min(start
- + numInterleavedColumns, sequenceLength)))
+ sb.append(s.getSequence(start,
+ Math.min(start + numInterleavedColumns, sequenceLength)))
.append(newline);
}
}
{
String seq = s[i].getSequenceAsString();
out.append(" Name: " + printId(s[i], jvsuffix) + " oo Len: "
- + seq.length()
- + " Check: " + checksums[i] + " Weight: 1.00");
+ + seq.length() + " Check: " + checksums[i]
+ + " Weight: 1.00");
out.append(newline);
if (seq.length() > max)
} catch (ExceptionPermissionDenied pdx)
{
errormessage = MessageManager.formatMessage(
- "exception.rnaml_couldnt_access_datasource",
- new String[] { pdx.getMessage() });
+ "exception.rnaml_couldnt_access_datasource", new String[]
+ { pdx.getMessage() });
throw new IOException(pdx);
} catch (ExceptionLoadingFailed lf)
{
errormessage = MessageManager.formatMessage(
- "exception.ranml_couldnt_process_data",
- new String[] { lf.getMessage() });
+ "exception.ranml_couldnt_process_data", new String[]
+ { lf.getMessage() });
throw new IOException(lf);
} catch (ExceptionFileFormatOrSyntax iff)
{
- errormessage = MessageManager.formatMessage(
- "exception.ranml_invalid_file",
- new String[] { iff.getMessage() });
+ errormessage = MessageManager
+ .formatMessage("exception.ranml_invalid_file", new String[]
+ { iff.getMessage() });
throw new IOException(iff);
} catch (Exception x)
{
error = true;
errormessage = MessageManager.formatMessage(
- "exception.ranml_problem_parsing_data",
- new String[] { x.getMessage() });
+ "exception.ranml_problem_parsing_data", new String[]
+ { x.getMessage() });
throw new IOException(errormessage, x);
}
}
@SuppressWarnings("unchecked")
- public void _parse() throws FileNotFoundException,
- ExceptionPermissionDenied, ExceptionLoadingFailed,
- ExceptionFileFormatOrSyntax
+ public void _parse()
+ throws FileNotFoundException, ExceptionPermissionDenied,
+ ExceptionLoadingFailed, ExceptionFileFormatOrSyntax
{
result = RNAFactory.loadSecStrRNAML(getReader());
}
for (int k = 0; k < rna.length(); k++)
{
- ann[k] = new Annotation(annot[k], "", Rna.getRNASecStrucState(
- annot[k]).charAt(0), 0f);
+ ann[k] = new Annotation(annot[k], "",
+ Rna.getRNASecStrucState(annot[k]).charAt(0), 0f);
}
AlignmentAnnotation align = new AlignmentAnnotation(
"Secondary Structure",
- current.getID().trim().length() > 0 ? "Secondary Structure for "
- + current.getID()
- : "", ann);
+ current.getID().trim().length() > 0
+ ? "Secondary Structure for " + current.getID()
+ : "",
+ ann);
sqs[i].addAlignmentAnnotation(align);
sqs[i].setRNA(result.get(i));
* and the substitution scores
* </pre>
*/
-public class ScoreMatrixFile extends AlignFile implements
- AlignmentFileReaderI
+public class ScoreMatrixFile extends AlignFile
+ implements AlignmentFileReaderI
{
// first non-comment line identifier - also checked in IdentifyFile
public static final String SCOREMATRIX = "SCOREMATRIX";
*/
if (row < size)
{
- err = String
- .format("Expected %d rows of score data in score matrix but only found %d",
- size, row);
+ err = String.format(
+ "Expected %d rows of score data in score matrix but only found %d",
+ size, row);
throw new FileFormatException(err);
}
String symbol = scoreLine.nextToken();
if (symbol.length() > 1 || symbol.charAt(0) != alphabet[row])
{
- err = String
- .format("Error parsing score matrix at line %d, expected '%s' but found '%s'",
- lineNo, alphabet[row], symbol);
+ err = String.format(
+ "Error parsing score matrix at line %d, expected '%s' but found '%s'",
+ lineNo, alphabet[row], symbol);
throw new FileFormatException(err);
}
tokenCount = scoreLine.countTokens(); // excluding guide symbol
err = String.format(
"Expected %d scores at line %d: '%s' but found %d", row + 1,
lineNo, data, tokenCount);
- throw new FileFormatException(err);
+ throw new FileFormatException(err);
}
if (!isLowerDiagonalOnly && tokenCount != size)
col++;
} catch (NumberFormatException e)
{
- err = String.format(
- "Invalid score value '%s' at line %d column %d", value,
- lineNo, col);
+ err = String.format("Invalid score value '%s' at line %d column %d",
+ value, lineNo, col);
throw new FileFormatException(err);
}
}
{
String err = "Unexpected aaIndex score matrix data at line " + lineNo
+ ": " + data;
-
+
try
{
String[] toks = data.split(",");
{
return 1;
}
- int comp = s1 == null ? -1 : (s2 == null ? 1 : s1
- .compareToIgnoreCase(s2));
+ int comp = s1 == null ? -1
+ : (s2 == null ? 1 : s1.compareToIgnoreCase(s2));
if (comp == 0)
{
String a1 = ref1.getAccessionId();
String a2 = ref2.getAccessionId();
- comp = a1 == null ? -1 : (a2 == null ? 1 : a1
- .compareToIgnoreCase(a2));
+ comp = a1 == null ? -1
+ : (a2 == null ? 1 : a1.compareToIgnoreCase(a2));
}
return comp;
}
sb.append("<br>");
}
sb.append(feature.getType()).append(" ").append(feature.getBegin())
- .append(":")
- .append(feature.getEnd());
+ .append(":").append(feature.getEnd());
}
}
else
// check score should be shown
if (!Float.isNaN(feature.getScore()))
{
- float[][] rng = (minmax == null) ? null : minmax.get(feature
- .getType());
+ float[][] rng = (minmax == null) ? null
+ : minmax.get(feature.getType());
if (rng != null && rng[0] != null && rng[0][0] != rng[0][1])
{
sb.append(" Score=").append(String.valueOf(feature.getScore()));
{
for (List<String> urllink : createLinksFrom(null, urlstring))
{
- sb.append("<br/> <a href=\""
- + urllink.get(3)
- + "\" target=\""
- + urllink.get(0)
- + "\">"
+ sb.append("<br/> <a href=\"" + urllink.get(3) + "\" target=\""
+ + urllink.get(0) + "\">"
+ (urllink.get(0).toLowerCase()
- .equals(urllink.get(1).toLowerCase()) ? urllink
- .get(0) : (urllink.get(0) + ":" + urllink
- .get(1)))
+ .equals(urllink.get(1).toLowerCase())
+ ? urllink.get(0)
+ : (urllink.get(0) + ":"
+ + urllink.get(1)))
+ "</a></br>");
}
} catch (Exception x)
{
- System.err.println("problem when creating links from "
- + urlstring);
+ System.err.println(
+ "problem when creating links from " + urlstring);
x.printStackTrace();
}
}
SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
Map<String, float[][]> minmax)
{
- int maxWidth = createSequenceAnnotationReport(tip, sequence,
- showDbRefs, showNpFeats, minmax, true);
+ int maxWidth = createSequenceAnnotationReport(tip, sequence, showDbRefs,
+ showNpFeats, minmax, true);
if (maxWidth > 60)
{
rstart = Long.parseLong(stindx);
} catch (Exception e)
{
- System.err.println("Couldn't parse '" + stindx
- + "' as start of row");
+ System.err.println(
+ "Couldn't parse '" + stindx + "' as start of row");
// inAlignments = false;
// warn for this line
}
rend = Long.parseLong(endindx);
} catch (Exception e)
{
- System.err.println("Couldn't parse '" + endindx
- + "' as end of row");
+ System.err.println(
+ "Couldn't parse '" + endindx + "' as end of row");
// inAlignments = false;
// warn for this line
{
padseq = true; // prepend gaps to new sequences in this block
seqentry = new Object[] { new StringBuffer(),
- new long[] { rstart, rend } };
+ new long[]
+ { rstart, rend } };
seqentries.addElement(seqentry);
seqhash.put(sqid, seqentry);
{
Sequence newseq = new Sequence(idstring,
- ((StringBuffer) seqentry[0]).toString(),
+ ((StringBuffer) seqentry[0]).toString(),
(int) ((long[]) seqentry[1])[0],
(int) ((long[]) seqentry[1])[1]);
if (newseq.getEnd() == 0)
for (int k = 0; k < rna.length(); k++)
{
- ann[k] = new Annotation(annot[k], "", Rna.getRNASecStrucState(
- annot[k]).charAt(0), 0f);
+ ann[k] = new Annotation(annot[k], "",
+ Rna.getRNASecStrucState(annot[k]).charAt(0), 0f);
}
AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",
r = new Regex("# STOCKHOLM ([\\d\\.]+)");
if (!r.search(nextLine()))
{
- throw new IOException(
- MessageManager
- .getString("exception.stockholm_invalid_format"));
+ throw new IOException(MessageManager
+ .getString("exception.stockholm_invalid_format"));
}
else
{
{
// logger.error("Could not parse sequence line: " + line);
throw new IOException(MessageManager.formatMessage(
- "exception.couldnt_parse_sequence_line",
- new String[] { line }));
+ "exception.couldnt_parse_sequence_line", new String[]
+ { line }));
}
String ns = seqs.get(x.stringMatched(1));
if (ns == null)
// }
else
{
- System.err
- .println("Warning - couldn't parse sequence annotation row line:\n"
+ System.err.println(
+ "Warning - couldn't parse sequence annotation row line:\n"
+ line);
// throw new IOException("Error parsing " + line);
}
else
{
throw new IOException(MessageManager.formatMessage(
- "exception.unknown_annotation_detected", new String[] {
- annType, annContent }));
+ "exception.unknown_annotation_detected", new String[]
+ { annType, annContent }));
}
}
}
{
for (DBRefEntry d : dbrs)
{
- jalview.util.MapList mp = new jalview.util.MapList(new int[] {
- seqO.getStart(), seqO.getEnd() }, new int[] { st, en }, 1, 1);
+ jalview.util.MapList mp = new jalview.util.MapList(
+ new int[]
+ { seqO.getStart(), seqO.getEnd() }, new int[] { st, en }, 1,
+ 1);
jalview.datamodel.Mapping mping = new Mapping(mp);
d.setMap(mping);
}
String type = label;
if (label.contains("_cons"))
{
- type = (label.indexOf("_cons") == label.length() - 5) ? label
- .substring(0, label.length() - 5) : label;
+ type = (label.indexOf("_cons") == label.length() - 5)
+ ? label.substring(0, label.length() - 5)
+ : label;
}
boolean ss = false, posterior = false;
type = id2type(type);
ann.secondaryStructure = ResidueProperties.getDssp3state(pos)
.charAt(0);
- if (ann.secondaryStructure == pos.charAt(0))
- {
- ann.displayCharacter = ""; // null; // " ";
- }
- else
- {
- ann.displayCharacter = " " + ann.displayCharacter;
- }
+ if (ann.secondaryStructure == pos.charAt(0))
+ {
+ ann.displayCharacter = ""; // null; // " ";
+ }
+ else
+ {
+ ann.displayCharacter = " " + ann.displayCharacter;
+ }
}
}
{
Object idd = en.nextElement();
String type = (String) dataRef.remove(idd);
- out.append(new Format("%-" + (maxid - 2) + "s").form("#=GS "
- + idd.toString() + " "));
+ out.append(new Format("%-" + (maxid - 2) + "s")
+ .form("#=GS " + idd.toString() + " "));
if (type.contains("PFAM") || type.contains("RFAM"))
{
}
// out.append("#=GR ");
- out.append(new Format("%-" + maxid + "s").form("#=GR "
- + printId(s[i], jvSuffix) + " " + key + " "));
+ out.append(new Format("%-" + maxid + "s").form(
+ "#=GR " + printId(s[i], jvSuffix) + " " + key + " "));
ann = alAnot[j].annotations;
String seq = "";
for (int k = 0; k < ann.length; k++)
}
label = label.replace(" ", "_");
- out.append(new Format("%-" + maxid + "s").form("#=GC " + label
- + " "));
+ out.append(
+ new Format("%-" + maxid + "s").form("#=GC " + label + " "));
boolean isrna = aa.isValidStruc();
for (int j = 0; j < aa.annotations.length; j++)
{
{
char seq = ' ';
Annotation annot = ann[k];
- String ch = (annot == null) ? ((sequenceI == null) ? "-" : Character
- .toString(sequenceI.getCharAt(k))) : annot.displayCharacter;
+ String ch = (annot == null)
+ ? ((sequenceI == null) ? "-"
+ : Character.toString(sequenceI.getCharAt(k)))
+ : annot.displayCharacter;
if (key != null && key.equals("SS"))
{
if (annot == null)
{
return (String) typeIds.get(id);
}
- System.err.println("Warning : Unknown Stockholm annotation type code "
- + id);
+ System.err.println(
+ "Warning : Unknown Stockholm annotation type code " + id);
return id;
}
{
return key;
}
- System.err.println("Warning : Unknown Stockholm annotation type: "
- + type);
+ System.err.println(
+ "Warning : Unknown Stockholm annotation type: " + type);
return key;
}
{
// TODO: use the PDB ID of the structure if one is available, to save
// bandwidth and avoid uploading the whole structure to the service
- Object annotate3d = cl.getConstructor(new Class[] {}).newInstance(
- new Object[] {});
- AlignmentI al = ((AlignmentI) cl.getMethod("getRNAMLFor",
- new Class[] { FileParse.class }).invoke(annotate3d,
- new Object[] { new FileParse(getDataName(), dataSourceType) }));
+ Object annotate3d = cl.getConstructor(new Class[] {})
+ .newInstance(new Object[] {});
+ AlignmentI al = ((AlignmentI) cl
+ .getMethod("getRNAMLFor", new Class[]
+ { FileParse.class })
+ .invoke(annotate3d, new Object[]
+ { new FileParse(getDataName(), dataSourceType) }));
for (SequenceI sq : al.getSequences())
{
if (sq.getDatasetSequence() != null)
}
@SuppressWarnings("unchecked")
- protected void replaceAndUpdateChains(List<SequenceI> prot,
- AlignmentI al, String pep, boolean b)
+ protected void replaceAndUpdateChains(List<SequenceI> prot, AlignmentI al,
+ String pep, boolean b)
{
List<List<? extends Object>> replaced = AlignSeq
.replaceMatchingSeqsWith(seqs, annotations, prot, al, pep,
processWithJmolParser(proteinSequences);
} catch (Exception x)
{
- System.err
- .println("Exceptions from Jmol when processing data in pdb file");
+ System.err.println(
+ "Exceptions from Jmol when processing data in pdb file");
x.printStackTrace();
}
}
Class cl = Class.forName("jalview.ext.jmol.JmolParser");
if (cl != null)
{
- final Constructor constructor = cl.getConstructor(new Class[] {FileParse.class });
- final Object[] args = new Object[] { new FileParse(getDataName(), dataSourceType) };
+ final Constructor constructor = cl
+ .getConstructor(new Class[]
+ { FileParse.class });
+ final Object[] args = new Object[] {
+ new FileParse(getDataName(), dataSourceType) };
StructureImportSettings.setShowSeqFeatures(false);
StructureImportSettings.setVisibleChainAnnotation(false);
StructureImportSettings
.setExternalSecondaryStructure(externalSecondaryStructure);
Object jmf = constructor.newInstance(args);
- AlignmentI al = new Alignment((SequenceI[]) cl.getMethod(
- "getSeqsAsArray", new Class[] {}).invoke(jmf));
+ AlignmentI al = new Alignment((SequenceI[]) cl
+ .getMethod("getSeqsAsArray", new Class[] {}).invoke(jmf));
cl.getMethod("addAnnotations", new Class[] { AlignmentI.class })
.invoke(jmf, al);
for (SequenceI sq : al.getSequences())
{
dataName = dataName.substring(p + 1);
}
- if(dataName.indexOf(".") > -1){
+ if (dataName.indexOf(".") > -1)
+ {
dataName = dataName.substring(0, dataName.lastIndexOf("."));
}
return dataName;
*/
public String getScoresFor(String id)
{
- return scores != null && scores.containsKey(id) ? scores.get(id)
- .toString() : "";
+ return scores != null && scores.containsKey(id)
+ ? scores.get(id).toString()
+ : "";
}
/**
if (scoreStringBuilder == null)
{
error = true;
- errormessage = String
- .format("Invalid T-Coffee score file: Sequence ID '%s' is not declared in header section",
- entry.getKey());
+ errormessage = String.format(
+ "Invalid T-Coffee score file: Sequence ID '%s' is not declared in header section",
+ entry.getKey());
return;
}
i++;
if (s == null && i != scores.size() && !id.getKey().equals("cons"))
{
- System.err.println("No "
- + (matchids ? "match " : " sequences left ")
- + " for TCoffee score set : " + id.getKey());
+ System.err
+ .println("No " + (matchids ? "match " : " sequences left ")
+ + " for TCoffee score set : " + id.getKey());
continue;
}
int jSize = al.getWidth() < srow.length ? al.getWidth() : srow.length;
annotations[j] = null;
if (val > 0)
{
- System.err
- .println("Warning: non-zero value for positional T-COFFEE score for gap at "
+ System.err.println(
+ "Warning: non-zero value for positional T-COFFEE score for gap at "
+ j + " in sequence " + s.getName());
}
}
else
{
annotations[j] = new Annotation(s == null ? "" + val : null,
- s == null ? "" + val : null, '\0', val * 1f, val >= 0
- && val < colors.length ? colors[val]
+ s == null ? "" + val : null, '\0', val * 1f,
+ val >= 0 && val < colors.length ? colors[val]
: Color.white);
}
}
Vobject obj = getjv2vObj(seqsetidobj);
if (obj != null && !(obj instanceof Alignment))
{
- Cache.log
- .warn("IMPLEMENTATION ERROR?: Unexpected mapping for unmapped jalview string object content:"
+ Cache.log.warn(
+ "IMPLEMENTATION ERROR?: Unexpected mapping for unmapped jalview string object content:"
+ seqsetidobj + " to object " + obj);
}
return obj;
if (Cache.log.isDebugEnabled())
{
- Cache.log.debug("Returning null VorbaID binding for jalview object "
- + jvobj);
+ Cache.log.debug(
+ "Returning null VorbaID binding for jalview object " + jvobj);
}
return null;
}
if (id == null)
{
id = cdoc.registerObject(vobj);
- Cache.log
- .debug("Registering new object and returning null for getvObj2jv");
+ Cache.log.debug(
+ "Registering new object and returning null for getvObj2jv");
return null;
}
if (vobj2jv.containsKey(vobj.getVorbaId()))
{
Cache.log.error("Failed to get id for "
+ (vobj.isRegisterable() ? "registerable"
- : "unregisterable") + " object " + vobj);
+ : "unregisterable")
+ + " object " + vobj);
}
}
if (vobj2jv.containsKey(vobj.getVorbaId())
&& !((VorbaId) vobj2jv.get(vobj.getVorbaId())).equals(jvobj))
{
- Cache.log
- .debug("Warning? Overwriting existing vamsas id binding for "
+ Cache.log.debug(
+ "Warning? Overwriting existing vamsas id binding for "
+ vobj.getVorbaId(),
- new Exception(
- MessageManager
- .getString("exception.overwriting_vamsas_id_binding")));
+ new Exception(MessageManager.getString(
+ "exception.overwriting_vamsas_id_binding")));
}
else if (jv2vobj.containsKey(jvobj)
&& !((VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))
{
Cache.log.debug(
"Warning? Overwriting existing jalview object binding for "
- + jvobj, new Exception(
- "Overwriting jalview object binding."));
+ + jvobj,
+ new Exception("Overwriting jalview object binding."));
}
/*
* Cache.log.error("Attempt to make conflicting object binding! "+vobj+" id "
if (vbound.getV_parent() != null
&& dataset != vbound.getV_parent())
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_cannot_map_alignment_sequences"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_cannot_map_alignment_sequences"));
// This occurs because the dataset for the alignment we are
// trying to
}
// flag.
// this *will* break when alignment contains both nucleotide and amino
// acid sequences.
- String dict = jal.isNucleotide() ? uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA
+ String dict = jal.isNucleotide()
+ ? uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA
: uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA;
Vector dssmods = new Vector();
for (int i = 0; i < jal.getHeight(); i++)
// referenced
// sequences
// to dataset.
- Datasetsequence dssync = new jalview.io.vamsas.Datasetsequence(
- this, sq, dict, dataset);
+ Datasetsequence dssync = new jalview.io.vamsas.Datasetsequence(this,
+ sq, dict, dataset);
sequence = (Sequence) dssync.getVobj();
if (dssync.getModified())
{
else
{
// always prepare to clone the alignment
- boolean alismod = av.isUndoRedoHashModified((long[]) alignRDHash
- .get(av.getSequenceSetId()));
+ boolean alismod = av.isUndoRedoHashModified(
+ (long[]) alignRDHash.get(av.getSequenceSetId()));
// todo: verify and update mutable alignment props.
// TODO: Use isLocked methods
if (alignment.getModifiable() == null
{
// removeValignmentSequences(alignment, docseqs);
docseqs.removeAllElements();
- System.out
- .println("Sequence deletion from alignment is not implemented.");
+ System.out.println(
+ "Sequence deletion from alignment is not implemented.");
}
if (modified)
// unbind alignment from view.
// create new binding and new alignment.
// mark trail on new alignment as being derived from old ?
- System.out
- .println("update edited alignment to new alignment in document.");
+ System.out.println(
+ "update edited alignment to new alignment in document.");
}
}
// ////////////////////////////////////////////
// SAVE Alignment Sequence Features
- for (int i = 0, iSize = alignment.getAlignmentSequenceCount(); i < iSize; i++)
+ for (int i = 0, iSize = alignment
+ .getAlignmentSequenceCount(); i < iSize; i++)
{
AlignmentSequence valseq;
- SequenceI alseq = (SequenceI) getvObj2jv(valseq = alignment
- .getAlignmentSequence(i));
+ SequenceI alseq = (SequenceI) getvObj2jv(
+ valseq = alignment.getAlignmentSequence(i));
if (alseq != null && alseq.getSequenceFeatures() != null)
{
/*
if (aa[i].groupRef != null)
{
// TODO: store any group associated annotation references
- Cache.log
- .warn("Group associated sequence annotation is not stored in VAMSAS document.");
+ Cache.log.warn(
+ "Group associated sequence annotation is not stored in VAMSAS document.");
continue;
}
if (aa[i].sequenceRef != null)
else
{
// add Alignment Annotation
- uk.ac.vamsas.objects.core.AlignmentAnnotation an = (uk.ac.vamsas.objects.core.AlignmentAnnotation) getjv2vObj(aa[i]);
+ uk.ac.vamsas.objects.core.AlignmentAnnotation an = (uk.ac.vamsas.objects.core.AlignmentAnnotation) getjv2vObj(
+ aa[i]);
if (an == null)
{
an = new uk.ac.vamsas.objects.core.AlignmentAnnotation();
ae = new AnnotationElement();
ae.setDescription(aa[i].annotations[a].description);
ae.addGlyph(new Glyph());
- ae.getGlyph(0).setContent(
- aa[i].annotations[a].displayCharacter); // assume
+ ae.getGlyph(0)
+ .setContent(aa[i].annotations[a].displayCharacter); // assume
// jax-b
// takes
// care
if (aa[i].annotations[a].secondaryStructure != ' ')
{
Glyph ss = new Glyph();
- ss.setDict(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
- ss.setContent(String
- .valueOf(aa[i].annotations[a].secondaryStructure));
+ ss.setDict(
+ uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
+ ss.setContent(String.valueOf(
+ aa[i].annotations[a].secondaryStructure));
ae.addGlyph(ss);
}
an.addAnnotationElement(ae);
if (aa[i].threshold != null && aa[i].threshold.displayed)
{
an.addProperty(Properties.newProperty(THRESHOLD,
- Properties.FLOATTYPE, "" + aa[i].threshold.value));
+ Properties.FLOATTYPE,
+ "" + aa[i].threshold.value));
if (aa[i].threshold.label != null)
{
- an.addProperty(Properties.newProperty(THRESHOLD
- + "Name", Properties.STRINGTYPE, ""
- + aa[i].threshold.label));
+ an.addProperty(Properties.newProperty(
+ THRESHOLD + "Name", Properties.STRINGTYPE,
+ "" + aa[i].threshold.label));
}
}
}
// LOCK METHODS)
{
// verify annotation - update (perhaps)
- Cache.log
- .info("update alignment sequence annotation. not yet implemented.");
+ Cache.log.info(
+ "update alignment sequence annotation. not yet implemented.");
}
else
{
// verify annotation - update (perhaps)
- Cache.log
- .info("updated alignment sequence annotation added.");
+ Cache.log.info(
+ "updated alignment sequence annotation added.");
}
}
}
* @param alignment
* @param docseqs
*/
- private void removeValignmentSequences(Alignment alignment, Vector docseqs)
+ private void removeValignmentSequences(Alignment alignment,
+ Vector docseqs)
{
// delete these from document. This really needs to be a generic document
// API function derived by CASTOR.
Enumeration en = docseqs.elements();
while (en.hasMoreElements())
{
- alignment.removeAlignmentSequence((AlignmentSequence) en
- .nextElement());
+ alignment.removeAlignmentSequence(
+ (AlignmentSequence) en.nextElement());
}
- Entry pe = addProvenance(alignment.getProvenance(), "Removed "
- + docseqs.size() + " sequences");
+ Entry pe = addProvenance(alignment.getProvenance(),
+ "Removed " + docseqs.size() + " sequences");
en = alignment.enumerateAlignmentAnnotation();
Vector toremove = new Vector();
while (en.hasMoreElements())
en = toremove.elements();
while (en.hasMoreElements())
{
- alignment
- .removeAlignmentAnnotation((uk.ac.vamsas.objects.core.AlignmentAnnotation) en
+ alignment.removeAlignmentAnnotation(
+ (uk.ac.vamsas.objects.core.AlignmentAnnotation) en
.nextElement());
}
// TODO: search through alignment annotations to remove any references to
modal = true;
alseq.setName(jvalsq.getName());
}
- if (jvalsq.getDescription() != null
- && (alseq.getDescription() == null || !jvalsq.getDescription()
- .equals(alseq.getDescription())))
+ if (jvalsq.getDescription() != null && (alseq.getDescription() == null
+ || !jvalsq.getDescription().equals(alseq.getDescription())))
{
modal = true;
alseq.setDescription(jvalsq.getDescription());
}
if (getjv2vObj(jvalsq.getDatasetSequence()) == null)
{
- Cache.log
- .warn("Serious Implementation error - Unbound dataset sequence in alignment: "
+ Cache.log.warn(
+ "Serious Implementation error - Unbound dataset sequence in alignment: "
+ jvalsq.getDatasetSequence());
}
alseq.setRefid(getjv2vObj(jvalsq.getDatasetSequence()));
|| !valseq.getSequence().equals(alseq.getSequenceAsString()))
{
// this might go *horribly* wrong
- alseq.setSequence(new String(valseq.getSequence()).replace(
- valGapchar, gapChar));
+ alseq.setSequence(new String(valseq.getSequence())
+ .replace(valGapchar, gapChar));
alseq.setStart((int) valseq.getStart());
alseq.setEnd((int) valseq.getEnd());
modal = true;
modal = true;
alseq.setName(valseq.getName());
}
- if (alseq.getDescription() == null
- || (valseq.getDescription() != null && !alseq
- .getDescription().equals(valseq.getDescription())))
+ if (alseq.getDescription() == null || (valseq.getDescription() != null
+ && !alseq.getDescription().equals(valseq.getDescription())))
{
alseq.setDescription(valseq.getDescription());
modal = true;
}
if (modal && Cache.log.isDebugEnabled())
{
- Cache.log.debug("Updating apparently edited sequence "
- + alseq.getName());
+ Cache.log.debug(
+ "Updating apparently edited sequence " + alseq.getName());
}
}
else
{
- alseq = new jalview.datamodel.Sequence(valseq.getName(), valseq
- .getSequence().replace(valGapchar, gapChar),
+ alseq = new jalview.datamodel.Sequence(valseq.getName(),
+ valseq.getSequence().replace(valGapchar, gapChar),
(int) valseq.getStart(), (int) valseq.getEnd());
Vobject datsetseq = (Vobject) valseq.getRefid();
// inherit description line from dataset.
if (alseq.getDatasetSequence().getDescription() != null)
{
- alseq.setDescription(alseq.getDatasetSequence()
- .getDescription());
+ alseq.setDescription(
+ alseq.getDatasetSequence().getDescription());
}
}
// if
}
else
{
- Cache.log
- .error("Invalid dataset sequence id (null) for alignment sequence "
+ Cache.log.error(
+ "Invalid dataset sequence id (null) for alignment sequence "
+ valseq.getVorbaId());
}
bindjvvobj(alseq, valseq);
{
// we only write an annotation where it really exists.
Glyph ss = new Glyph();
- ss.setDict(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
- ss.setContent(String
- .valueOf(alan.annotations[a].secondaryStructure));
+ ss.setDict(
+ uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
+ ss.setContent(
+ String.valueOf(alan.annotations[a].secondaryStructure));
ae.addGlyph(ss);
}
an.addAnnotationElement(ae);
// uk.ac.vamsas.
// objects.core.AlignmentSequence alsref = (uk.ac.vamsas.
// objects.core.AlignmentSequence) sref;
- uk.ac.vamsas.objects.core.DataSetAnnotations an = (uk.ac.vamsas.objects.core.DataSetAnnotations) getjv2vObj(alan);
+ uk.ac.vamsas.objects.core.DataSetAnnotations an = (uk.ac.vamsas.objects.core.DataSetAnnotations) getjv2vObj(
+ alan);
int[] gapMap = getGapMap(AlSeqMaps, alan);
if (an == null)
{
else
{
// verify existing alignment sequence annotation is up to date
- System.out
- .println("make new alignment dataset sequence annotation if modification has happened.");
+ System.out.println(
+ "make new alignment dataset sequence annotation if modification has happened.");
}
}
// uk.ac.vamsas.
// objects.core.AlignmentSequence alsref = (uk.ac.vamsas.
// objects.core.AlignmentSequence) sref;
- uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation an = (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) getjv2vObj(alan);
+ uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation an = (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) getjv2vObj(
+ alan);
int[] gapMap = getGapMap(AlSeqMaps, alan);
if (an == null)
{
else
{
// verify existing alignment sequence annotation is up to date
- System.out
- .println("make new alignment sequence annotation if modification has happened.");
+ System.out.println(
+ "make new alignment sequence annotation if modification has happened.");
}
}
}
@Override
public JarInputStream getJarInputStream() throws IOException
{
- jalview.bin.Cache.log
- .debug("Returning client input stream for Jalview from Vamsas Document.");
+ jalview.bin.Cache.log.debug(
+ "Returning client input stream for Jalview from Vamsas Document.");
return new JarInputStream(cappdata.getClientInputStream());
}
};
@Override
public JarInputStream getJarInputStream() throws IOException
{
- jalview.bin.Cache.log
- .debug("Returning user input stream for Jalview from Vamsas Document.");
+ jalview.bin.Cache.log.debug(
+ "Returning user input stream for Jalview from Vamsas Document.");
return new JarInputStream(cappdata.getUserInputStream());
}
};
// TODO implement this : af.getNumberOfViews
String seqsetidobj = av.getSequenceSetId();
views = Desktop.getViewports(seqsetidobj);
- Cache.log.debug("Found "
- + (views == null ? " no " : "" + views.length)
- + " views for '" + av.getSequenceSetId() + "'");
+ Cache.log
+ .debug("Found " + (views == null ? " no " : "" + views.length)
+ + " views for '" + av.getSequenceSetId() + "'");
if (views.length > 1)
{
// we need to close the original document view.
// from another client
throw new Error(MessageManager.formatMessage(
"error.implementation_error_old_jalview_object_not_bound",
- new String[] { oldjvobject.toString() }));
+ new String[]
+ { oldjvobject.toString() }));
}
if (newjvobject != null)
{
jxml.setSkipList(skipList);
if (dojvsync)
{
- jxml.saveState(new JarOutputStream(cappdata
- .getClientOutputStream()));
+ jxml.saveState(
+ new JarOutputStream(cappdata.getClientOutputStream()));
}
} catch (Exception e)
{
// TODO raise GUI warning if user requests it.
- jalview.bin.Cache.log
- .error("Couldn't update jalview client application data. Giving up - local settings probably lost.",
- e);
+ jalview.bin.Cache.log.error(
+ "Couldn't update jalview client application data. Giving up - local settings probably lost.",
+ e);
}
}
else
{
- jalview.bin.Cache.log
- .error("Couldn't access client application data for vamsas session. This is probably a vamsas client bug.");
+ jalview.bin.Cache.log.error(
+ "Couldn't access client application data for vamsas session. This is probably a vamsas client bug.");
}
}
DataSet dataset = root.getDataSet(_ds);
int i, iSize = dataset.getSequenceCount();
List<SequenceI> dsseqs;
- jalview.datamodel.Alignment jdataset = (jalview.datamodel.Alignment) getvObj2jv(dataset);
+ jalview.datamodel.Alignment jdataset = (jalview.datamodel.Alignment) getvObj2jv(
+ dataset);
int jremain = 0;
if (jdataset == null)
{
// add any new dataset sequence feature annotations
if (dataset.getDataSetAnnotations() != null)
{
- for (int dsa = 0; dsa < dataset.getDataSetAnnotationsCount(); dsa++)
+ for (int dsa = 0; dsa < dataset
+ .getDataSetAnnotationsCount(); dsa++)
{
DataSetAnnotations dseta = dataset.getDataSetAnnotations(dsa);
// TODO: deal with group annotation on datset sequences.
if (dseta.getSeqRefCount() == 1)
{
- SequenceI dsSeq = (SequenceI) getvObj2jv((Vobject) dseta
- .getSeqRef(0)); // TODO: deal with group dataset
+ SequenceI dsSeq = (SequenceI) getvObj2jv(
+ (Vobject) dseta.getSeqRef(0)); // TODO: deal with group
+ // dataset
// annotations
if (dsSeq == null)
{
- jalview.bin.Cache.log
- .warn("Couldn't resolve jalview sequenceI for dataset object reference "
- + ((Vobject) dataset.getDataSetAnnotations(
- dsa).getSeqRef(0)).getVorbaId()
- .getId());
+ jalview.bin.Cache.log.warn(
+ "Couldn't resolve jalview sequenceI for dataset object reference "
+ + ((Vobject) dataset
+ .getDataSetAnnotations(dsa)
+ .getSeqRef(0)).getVorbaId()
+ .getId());
}
else
{
// JBPNote: we could just add them to all alignments but
// that may complicate cross references in the jalview
// datamodel
- Cache.log
- .warn("Ignoring dataset annotation with annotationElements. Not yet supported in jalview.");
+ Cache.log.warn(
+ "Ignoring dataset annotation with annotationElements. Not yet supported in jalview.");
}
}
}
else
{
- Cache.log
- .warn("Ignoring multiply referenced dataset sequence annotation for binding to datsaet sequence features.");
+ Cache.log.warn(
+ "Ignoring multiply referenced dataset sequence annotation for binding to datsaet sequence features.");
}
}
}
{
// LOAD ALIGNMENTS from DATASET
- for (int al = 0, nal = dataset.getAlignmentCount(); al < nal; al++)
+ for (int al = 0, nal = dataset
+ .getAlignmentCount(); al < nal; al++)
{
uk.ac.vamsas.objects.core.Alignment alignment = dataset
.getAlignment(al);
// TODO check that correct alignment object is retrieved when
// hidden seqs exist.
jal = (av.hasHiddenRows()) ? av.getAlignment()
- .getHiddenSequences().getFullAlignment() : av
- .getAlignment();
+ .getHiddenSequences().getFullAlignment()
+ : av.getAlignment();
}
iSize = alignment.getAlignmentSequenceCount();
boolean refreshal = false;
for (i = 0; i < iSize; i++)
{
AlignmentSequence valseq = alignment.getAlignmentSequence(i);
- jalview.datamodel.Sequence alseq = (jalview.datamodel.Sequence) getvObj2jv(valseq);
+ jalview.datamodel.Sequence alseq = (jalview.datamodel.Sequence) getvObj2jv(
+ valseq);
if (syncFromAlignmentSequence(valseq, valGapchar, gapChar,
dsseqs) && alseq != null)
{
.getAlignmentSequenceAnnotation();
for (int a = 0; a < vasannot.length; a++)
{
- jalview.datamodel.AlignmentAnnotation asa = (jalview.datamodel.AlignmentAnnotation) getvObj2jv(vasannot[a]); // TODO:
+ jalview.datamodel.AlignmentAnnotation asa = (jalview.datamodel.AlignmentAnnotation) getvObj2jv(
+ vasannot[a]); // TODO:
// 1:many
// jalview
// alignment
// OBJECT LOCK
// METHODS)
{
- Cache.log
- .info("UNIMPLEMENTED: not recovering user modifiable sequence alignment annotation");
+ Cache.log.info(
+ "UNIMPLEMENTED: not recovering user modifiable sequence alignment annotation");
// TODO: should at least replace with new one - otherwise
// things will break
// basically do this:
if (newasAnnots != null && newasAnnots.size() > 0)
{
// Add the new sequence annotations in to the alignment.
- for (int an = 0, anSize = newasAnnots.size(); an < anSize; an++)
+ for (int an = 0, anSize = newasAnnots
+ .size(); an < anSize; an++)
{
- jal.addAnnotation((AlignmentAnnotation) newasAnnots
- .elementAt(an));
+ jal.addAnnotation(
+ (AlignmentAnnotation) newasAnnots.elementAt(an));
// TODO: check if anything has to be done - like calling
// adjustForAlignment or something.
newasAnnots.setElementAt(null, an);
for (int j = 0; j < an.length; j++)
{
- jalview.datamodel.AlignmentAnnotation jan = (jalview.datamodel.AlignmentAnnotation) getvObj2jv(an[j]);
+ jalview.datamodel.AlignmentAnnotation jan = (jalview.datamodel.AlignmentAnnotation) getvObj2jv(
+ an[j]);
if (jan != null)
{
// update or stay the same.
// jan.update(getjAlignmentAnnotation(jal, an[a])); // update
// from another annotation object in place.
- Cache.log
- .debug("update from vamsas alignment annotation to existing jalview alignment annotation.");
+ Cache.log.debug(
+ "update from vamsas alignment annotation to existing jalview alignment annotation.");
if (an[j].getModifiable() == null) // TODO: USE VAMSAS
// LIBRARY OBJECT LOCK
// METHODS)
{
// TODO: user defined annotation is totally mutable... - so
// load it up or throw away if locally edited.
- Cache.log
- .info("NOT IMPLEMENTED - Recovering user-modifiable annotation - yet...");
+ Cache.log.info(
+ "NOT IMPLEMENTED - Recovering user-modifiable annotation - yet...");
}
// TODO: compare annotation element rows
// TODO: compare props.
// ///////////////////////////////
// construct alignment view
alignFrame = new AlignFrame(jal, AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT, alignment.getVorbaId()
- .toString());
+ AlignFrame.DEFAULT_HEIGHT,
+ alignment.getVorbaId().toString());
av = alignFrame.getViewport();
newAlignmentViews.addElement(av);
- String title = alignment
- .getProvenance()
+ String title = alignment.getProvenance()
.getEntry(
alignment.getProvenance().getEntryCount() - 1)
.getAction();
if (alignment.getPropertyCount() > 0)
{
- for (int p = 0, pe = alignment.getPropertyCount(); p < pe; p++)
+ for (int p = 0, pe = alignment
+ .getPropertyCount(); p < pe; p++)
{
if (alignment.getProperty(p).getName().equals("title"))
{
DataSet dataset = root.getDataSet(_ds);
if (dataset.getSequenceMappingCount() > 0)
{
- for (int sm = 0, smCount = dataset.getSequenceMappingCount(); sm < smCount; sm++)
+ for (int sm = 0, smCount = dataset
+ .getSequenceMappingCount(); sm < smCount; sm++)
{
Rangetype seqmap = new jalview.io.vamsas.Sequencemapping(this,
dataset.getSequenceMapping(sm));
// may not quite cope with this (without binding an array of annotations to
// a vamsas alignment annotation)
// summary flags saying what we found over the set of annotation rows.
- boolean[] AeContent = new boolean[] { false, false, false, false, false };
+ boolean[] AeContent = new boolean[] { false, false, false, false,
+ false };
int[] rangeMap = getMapping(annotation);
- jalview.datamodel.Annotation[][] anot = new jalview.datamodel.Annotation[][]
- { new jalview.datamodel.Annotation[rangeMap.length],
+ jalview.datamodel.Annotation[][] anot = new jalview.datamodel.Annotation[][] {
+ new jalview.datamodel.Annotation[rangeMap.length],
new jalview.datamodel.Annotation[rangeMap.length] };
boolean mergeable = true; // false if 'after positions cant be placed on
// same annotation row as positions.
Glyph[] glyphs = ae[aa].getGlyph();
for (int g = 0; g < glyphs.length; g++)
{
- if (glyphs[g]
- .getDict()
- .equals(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE))
+ if (glyphs[g].getDict().equals(
+ uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE))
{
ss = glyphs[g].getContent();
AeContent[HASSECSTR] = true;
}
- else if (glyphs[g]
- .getDict()
- .equals(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_HD_HYDRO))
+ else if (glyphs[g].getDict().equals(
+ uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_HD_HYDRO))
{
Cache.log.debug("ignoring hydrophobicity glyph marker.");
AeContent[HASHPHOB] = true;
}
else
{
- Cache.log
- .debug("IMPLEMENTATION TODO: Ignoring unknown glyph type "
+ Cache.log.debug(
+ "IMPLEMENTATION TODO: Ignoring unknown glyph type "
+ glyphs[g].getDict());
}
}
AeContent[HASVALS] = true;
if (ae[aa].getValueCount() > 1)
{
- Cache.log.warn("ignoring additional "
- + (ae[aa].getValueCount() - 1)
- + " values in annotation element.");
+ Cache.log.warn(
+ "ignoring additional " + (ae[aa].getValueCount() - 1)
+ + " values in annotation element.");
}
val = ae[aa].getValue(0);
}
{
if (gl == null)
{
- gl = new GraphLine(val.floatValue(), "", java.awt.Color.black);
+ gl = new GraphLine(val.floatValue(), "",
+ java.awt.Color.black);
}
else
{
}
if (parsedRangeAnnotation == null)
{
- Cache.log
- .debug("Inserting empty annotation row elements for a whole-alignment annotation.");
+ Cache.log.debug(
+ "Inserting empty annotation row elements for a whole-alignment annotation.");
}
else
{
&& arow[i].description.length() < 3)
{
// copy over the description as the display char.
- arow[i].displayCharacter = new String(arow[i].description);
+ arow[i].displayCharacter = new String(
+ arow[i].description);
}
}
else
}
} catch (Exception e)
{
- Cache.log
- .info("UNIMPLEMENTED : Couldn't parse non-integer group value for setting graphGroup correctly.");
+ Cache.log.info(
+ "UNIMPLEMENTED : Couldn't parse non-integer group value for setting graphGroup correctly.");
}
return jan;
int[] se = null;
if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
{
- throw new Error(
- MessageManager
- .getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
+ throw new Error(MessageManager.getString(
+ "error.invalid_vamsas_rangetype_cannot_resolve_lists"));
}
if (dseta.getSegCount() > 0)
{
int[] se = null;
if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
{
- throw new Error(
- MessageManager
- .getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
+ throw new Error(MessageManager.getString(
+ "error.invalid_vamsas_rangetype_cannot_resolve_lists"));
}
if (dseta.getSegCount() > 0)
{
* @param maprange
* where the from range is the local mapped range, and the to range
* is the 'mapped' range in the MapRangeType
- * @param default unit for local
- * @param default unit for mapped
+ * @param default
+ * unit for local
+ * @param default
+ * unit for mapped
* @return MapList
*/
private jalview.util.MapList parsemapType(MapType maprange, int localu,
int[] mappedRange = getMapping(maprange.getMapped());
long lu = maprange.getLocal().hasUnit() ? maprange.getLocal().getUnit()
: localu;
- long mu = maprange.getMapped().hasUnit() ? maprange.getMapped()
- .getUnit() : mappedu;
+ long mu = maprange.getMapped().hasUnit()
+ ? maprange.getMapped().getUnit()
+ : mappedu;
ml = new jalview.util.MapList(localRange, mappedRange, (int) lu,
(int) mu);
return ml;
jalview.datamodel.Provenance jprov = new jalview.datamodel.Provenance();
for (int i = 0; i < prov.getEntryCount(); i++)
{
- jprov.addEntry(prov.getEntry(i).getUser(), prov.getEntry(i)
- .getAction(), prov.getEntry(i).getDate(), prov.getEntry(i)
- .getId());
+ jprov.addEntry(prov.getEntry(i).getUser(),
+ prov.getEntry(i).getAction(), prov.getEntry(i).getDate(),
+ prov.getEntry(i).getId());
}
return jprov;
return vobj2jv;
}
- public void storeSequenceMappings(AlignmentViewport viewport, String title)
- throws Exception
+ public void storeSequenceMappings(AlignmentViewport viewport,
+ String title) throws Exception
{
AlignmentViewport av = viewport;
try
Cache.log.warn("Creating new dataset for an alignment.");
jal.setDataset(null);
}
- dataset = (DataSet) ((Alignment) getjv2vObj(viewport
- .getSequenceSetId())).getV_parent(); // jal.getDataset());
+ dataset = (DataSet) ((Alignment) getjv2vObj(
+ viewport.getSequenceSetId())).getV_parent(); // jal.getDataset());
if (dataset == null)
{
dataset = (DataSet) getjv2vObj(jal.getDataset());
- Cache.log
- .error("Can't find the correct dataset for the alignment in this view. Creating new one.");
+ Cache.log.error(
+ "Can't find the correct dataset for the alignment in this view. Creating new one.");
}
// Store any sequence mappings.
jalview.datamodel.Mapping[] mps = acf.getProtMappings();
for (int smp = 0; smp < mps.length; smp++)
{
- uk.ac.vamsas.objects.core.SequenceType mfrom = (SequenceType) getjv2vObj(dmps[smp]);
+ uk.ac.vamsas.objects.core.SequenceType mfrom = (SequenceType) getjv2vObj(
+ dmps[smp]);
if (mfrom != null)
{
- new jalview.io.vamsas.Sequencemapping(this, mps[smp],
- mfrom, dataset);
+ new jalview.io.vamsas.Sequencemapping(this, mps[smp], mfrom,
+ dataset);
}
else
{
- Cache.log
- .warn("NO Vamsas Binding for local sequence! NOT CREATING MAPPING FOR "
- + dmps[smp].getDisplayId(true)
- + " to "
+ Cache.log.warn(
+ "NO Vamsas Binding for local sequence! NOT CREATING MAPPING FOR "
+ + dmps[smp].getDisplayId(true) + " to "
+ mps[smp].getTo().getName());
}
}
} catch (Exception e)
{
throw new Exception(MessageManager.formatMessage(
- "exception.couldnt_store_sequence_mappings",
- new String[] { title }), e);
+ "exception.couldnt_store_sequence_mappings", new String[]
+ { title }), e);
}
}
{
this.ap = ap;
this.al = al;
- output.setText(MessageManager
- .getString("label.wswublast_client_credits"));
+ output.setText(
+ MessageManager.getString("label.wswublast_client_credits"));
- Desktop.addInternalFrame(output, MessageManager
- .getString("label.blasting_for_unidentified_sequence"), 800,
- 300);
+ Desktop.addInternalFrame(output, MessageManager.getString(
+ "label.blasting_for_unidentified_sequence"), 800, 300);
for (int i = 0; i < ids.size(); i++)
{
{
identitiesFound = true;
- int value = Integer.parseInt(data.substring(
- data.indexOf("(") + 1, data.indexOf("%")));
+ int value = Integer.parseInt(data
+ .substring(data.indexOf("(") + 1, data.indexOf("%")));
if (value >= maxFound)
{
if (entries != null)
{
oldseq.addDBRef(new jalview.datamodel.DBRefEntry(
- jalview.datamodel.DBRefSource.UNIPROT, "0", entries[0]
- .getAccessionId()));
+ jalview.datamodel.DBRefSource.UNIPROT, "0",
+ entries[0].getAccessionId()));
}
}
}
for (int i = 0; i < 9; i++)
{
- java.net.URL url = getClass().getResource(
- "/images/dna" + (i + 1) + ".gif");
+ java.net.URL url = getClass()
+ .getResource("/images/dna" + (i + 1) + ".gif");
if (url != null)
{
output.setFrameIcon(imageIcon[imageIndex]);
output.setTitle(MessageManager.formatMessage(
"label.blasting_for_unidentified_sequence_jobs_running",
- new String[] { Integer.valueOf(jobsRunning).toString() }));
+ new String[]
+ { Integer.valueOf(jobsRunning).toString() }));
} catch (Exception ex)
{
}
package jalview.io.cache;
-
import jalview.bin.Cache;
import java.util.Hashtable;
private static final String DEFAULT_LIMIT_KEY = ".DEFAULT_LIMIT";
-
-
private Hashtable<String, LinkedHashSet<String>> cacheItems;
private AppCache()
return foundCache;
}
-
/**
* Returns a singleton instance of AppCache
*
return instance;
}
-
-
/**
* Method for persisting cache items for a given cache key
*
super();
this.cacheKey = newCacheKey;
setEditable(true);
- setPrototypeDisplayValue("XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
+ setPrototypeDisplayValue(
+ "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
appCache = AppCache.getInstance();
initCachePopupMenu();
initCache(newCacheKey);
return;
}
// convert delimited cache items to a list of strings
- List<String> persistedCacheItems = Arrays.asList(delimitedCacheStr
- .split(AppCache.CACHE_DELIMITER));
+ List<String> persistedCacheItems = Arrays
+ .asList(delimitedCacheStr.split(AppCache.CACHE_DELIMITER));
LinkedHashSet<String> foundCacheItems = appCache
.getAllCachedItemsFor(cacheKey);
{
pnlDefaultCache.setBackground(Color.WHITE);
// pad panel so as to align with other menu items
- pnlDefaultCache.setBorder(BorderFactory.createEmptyBorder(0,
- LEFT_BOARDER_WIDTH, 0, 0));
+ pnlDefaultCache.setBorder(
+ BorderFactory.createEmptyBorder(0, LEFT_BOARDER_WIDTH, 0, 0));
txtDefaultCacheSize.setPreferredSize(new Dimension(45, 20));
txtDefaultCacheSize.setFont(new java.awt.Font("Verdana", 0, 12));
- lblDefaultCacheSize.setText(MessageManager
- .getString("label.default_cache_size"));
+ lblDefaultCacheSize
+ .setText(MessageManager.getString("label.default_cache_size"));
lblDefaultCacheSize.setFont(new java.awt.Font("Verdana", 0, 12));
// Force input to accept only Integer entries up to length - INPUT_LIMIT
txtDefaultCacheSize.setDocument(new PlainDocument()
pnlDefaultCache.add(lblDefaultCacheSize);
menuItemClearCache.setFont(new java.awt.Font("Verdana", 0, 12));
pnlDefaultCache.add(txtDefaultCacheSize);
- menuItemClearCache.setText(MessageManager
- .getString("action.clear_cached_items"));
+ menuItemClearCache
+ .setText(MessageManager.getString("action.clear_cached_items"));
menuItemClearCache.addActionListener(new ActionListener()
{
@Override
@Override
public void run()
{
- int userLimit = txtDefaultCacheSize.getText().trim().isEmpty() ? Integer
- .valueOf(AppCache.DEFAULT_LIMIT) : Integer
- .valueOf(txtDefaultCacheSize.getText());
+ int userLimit = txtDefaultCacheSize.getText().trim().isEmpty()
+ ? Integer.valueOf(AppCache.DEFAULT_LIMIT)
+ : Integer.valueOf(txtDefaultCacheSize.getText());
int cacheLimit = appCache.updateCacheLimit(cacheKey, userLimit);
String userInput = getUserInput();
if (userInput != null && !userInput.isEmpty())
});
}
-
/**
* This method should be called to persist the in-memory cache when this
* components parent frame is closed / exited
public void persistCache()
{
appCache.persistCache(cacheKey);
- int userLimit = txtDefaultCacheSize.getText().trim().isEmpty() ? Integer
- .valueOf(AppCache.DEFAULT_LIMIT) : Integer
- .valueOf(txtDefaultCacheSize.getText());
+ int userLimit = txtDefaultCacheSize.getText().trim().isEmpty()
+ ? Integer.valueOf(AppCache.DEFAULT_LIMIT)
+ : Integer.valueOf(txtDefaultCacheSize.getText());
appCache.updateCacheLimit(cacheKey, userLimit);
}
*/
public String getUserInput()
{
- return getEditor().getItem() == null ? "" : getEditor().getItem()
- .toString().trim();
+ return getEditor().getItem() == null ? ""
+ : getEditor().getItem().toString().trim();
}
}
SequenceI mapFromSequence = seq;
SequenceI mapToSequence = mappedSequence;
if ((type == MappingType.NucleotideToPeptide && featureIsOnTarget)
- || (type == MappingType.PeptideToNucleotide && !featureIsOnTarget))
+ || (type == MappingType.PeptideToNucleotide
+ && !featureIsOnTarget))
{
mapFromSequence = mappedSequence;
mapToSequence = seq;
{
fromStart = alignToStart;
toStart = alignFromStart;
- toEnd = forwardStrand ? toStart + alignCount - 1 : toStart
- - (alignCount - 1);
+ toEnd = forwardStrand ? toStart + alignCount - 1
+ : toStart - (alignCount - 1);
int toLength = Math.abs(toEnd - toStart) + 1;
int fromLength = toLength * type.getFromRatio() / type.getToRatio();
fromEnd = fromStart + fromLength - 1;
*/
if ("-".equals(strand))
{
- System.err
- .println("Skipping mapping from reverse complement as not yet supported");
+ System.err.println(
+ "Skipping mapping from reverse complement as not yet supported");
return null;
}
* @return
*/
@SuppressWarnings("unused")
- protected String findTargetId(String target, Map<String, List<String>> set)
+ protected String findTargetId(String target,
+ Map<String, List<String>> set)
{
return target;
}
* @throws IOException
*/
protected SequenceFeature processProteinMatch(
- Map<String, List<String>> set, SequenceI seq,
- String[] gffColumns, AlignmentI align, List<SequenceI> newseqs,
+ Map<String, List<String>> set, SequenceI seq, String[] gffColumns,
+ AlignmentI align, List<SequenceI> newseqs,
boolean relaxedIdMatching)
{
// This is currently tailored to InterProScan GFF output:
* renamed with its qualified accession id; renaming has to wait until
* all sequence reference resolution is complete
*/
- String accessionId = StringUtils.listToDelimitedString(
- set.get(NAME), ",");
+ String accessionId = StringUtils
+ .listToDelimitedString(set.get(NAME), ",");
if (accessionId.length() > 0)
{
String database = sf.getType(); // TODO InterProScan only??
* restrict from range to make them match up
* it's kind of arbitrary which end we truncate - here it is the end
*/
- System.err.print("Truncating mapping from " + Arrays.toString(from)
- + " to ");
+ System.err.print(
+ "Truncating mapping from " + Arrays.toString(from) + " to ");
if (from[1] > from[0])
{
from[1] -= fromOverlap / toRatio;
/*
* restrict to range to make them match up
*/
- System.err.print("Truncating mapping to " + Arrays.toString(to)
- + " to ");
+ System.err.print(
+ "Truncating mapping to " + Arrays.toString(to) + " to ");
if (to[1] > to[0])
{
to[1] -= fromOverlap / fromRatio;
/**
* Parses the input line to a map of name / value(s) pairs. For example the
* line <br>
- * Notes=Fe-S;Method=manual curation, prediction; source = Pfam; Notes = Metal <br>
+ * Notes=Fe-S;Method=manual curation, prediction; source = Pfam; Notes = Metal
+ * <br>
* if parsed with delimiter=";" and separators {' ', '='} <br>
* would return a map with { Notes={Fe=S, Metal}, Method={manual curation,
* prediction}, source={Pfam}} <br>
*/
for (Entry<String, List<String>> attr : attributes.entrySet())
{
- String values = StringUtils.listToDelimitedString(
- attr.getValue(), ",");
+ String values = StringUtils.listToDelimitedString(attr.getValue(),
+ ",");
sf.setValue(attr.getKey(), values);
if (NOTE.equals(attr.getKey()))
{
}
/**
- *
- */
+ *
+ */
@Override
protected SequenceFeature buildSequenceFeature(String[] gff,
Map<String, List<String>> attributes)
SequenceOntologyI so = SequenceOntologyFactory.getInstance();
String type = columns[TYPE_COL];
if (so.isA(type, SequenceOntologyI.PROTEIN_MATCH)
- || (".".equals(columns[SOURCE_COL]) && so.isA(type,
- SequenceOntologyI.POLYPEPTIDE)))
+ || (".".equals(columns[SOURCE_COL])
+ && so.isA(type, SequenceOntologyI.POLYPEPTIDE)))
{
return true;
}
* GFF field 'ID' rather than the usual 'Target' :-O
*/
@Override
- protected String findTargetId(String target, Map<String, List<String>> set)
+ protected String findTargetId(String target,
+ Map<String, List<String>> set)
{
List<String> ids = set.get(ID);
if (ids == null || ids.size() != 1)
{
jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(src);
context.updateSetModified(ff.parse(context.getLastAlignment(),
- context.featureColours, false, context.relaxedIdMatching));
+ context.featureColours, false,
+ context.relaxedIdMatching));
} catch (Exception e)
{
errmsg = ("Failed to parse the Features file associated with the alignment.");
{
String type = args[i++];
final String file = args[i++];
- final JvDataType jtype = DataProvider.JvDataType.valueOf(type
- .toUpperCase());
+ final JvDataType jtype = DataProvider.JvDataType
+ .valueOf(type.toUpperCase());
if (jtype != null)
{
final FileParse fp;
ParsePackedSet pps;
try
{
- newdm = (pps = new ParsePackedSet()).getAlignment(
- context = new JalviewDataset(), dp);
+ newdm = (pps = new ParsePackedSet())
+ .getAlignment(context = new JalviewDataset(), dp);
} catch (Exception e)
{
System.out.println("Test failed for these arguments.\n");
{
if (context.getLastAlignmentSet().isModified())
{
- System.err
- .println("Initial alignment set was modified and any associated views should be updated.");
+ System.err.println(
+ "Initial alignment set was modified and any associated views should be updated.");
}
}
}
SequenceI sequence = (SequenceI) jvobj;
if (!sequence.getSequenceAsString().equals(sq.getSequence()))
{
- log.warn("Potential Client Error ! - mismatch of dataset sequence: and jalview internal dataset sequence.");
+ log.warn(
+ "Potential Client Error ! - mismatch of dataset sequence: and jalview internal dataset sequence.");
}
else
{
{
modified |= new jalview.io.vamsas.Sequencefeature(datastore,
(jalview.datamodel.SequenceFeature) sq
- .getSequenceFeatures()[sf], dataset,
- (Sequence) vobj).docWasUpdated();
+ .getSequenceFeatures()[sf],
+ dataset, (Sequence) vobj).docWasUpdated();
}
}
return modified;
for (int db = 0; db < entries.length; db++)
{
modifiedthedoc |= new jalview.io.vamsas.Dbref(datastore,
- // dbentry =
+ // dbentry =
entries[db], sq, (Sequence) vobj, dataset).docWasUpdated();
}
for (int db = 0; db < entries.length; db++)
{
modifiedtheseq |= new jalview.io.vamsas.Dbref(datastore,
- // dbentry =
+ // dbentry =
entries[db], vsq, sq).jvWasUpdated();
}
}
public void conflict()
{
- log.warn("Conflict in dataset sequence update to document. Overwriting document");
+ log.warn(
+ "Conflict in dataset sequence update to document. Overwriting document");
// TODO: could try to import from document data to jalview first. and then
updateToDoc();
}
}
if (Cache.log.isDebugEnabled())
{
- Cache.log.debug("Returning null VorbaID binding for jalview object "
- + jvobj);
+ Cache.log.debug(
+ "Returning null VorbaID binding for jalview object " + jvobj);
}
return null;
}
if (id == null)
{
id = cdoc.registerObject(vobj);
- Cache.log
- .debug("Registering new object and returning null for getvObj2jv");
+ Cache.log.debug(
+ "Registering new object and returning null for getvObj2jv");
return null;
}
if (vobj2jv.containsKey(vobj.getVorbaId()))
{
Cache.log.error("Failed to get id for "
+ (vobj.isRegisterable() ? "registerable"
- : "unregisterable") + " object " + vobj);
+ : "unregisterable")
+ + " object " + vobj);
}
}
if (vobj2jv.containsKey(vobj.getVorbaId())
&& !(vobj2jv.get(vobj.getVorbaId())).equals(jvobj))
{
- Cache.log
- .debug("Warning? Overwriting existing vamsas id binding for "
+ Cache.log.debug(
+ "Warning? Overwriting existing vamsas id binding for "
+ vobj.getVorbaId(),
- new Exception(
- MessageManager
- .getString("exception.overwriting_vamsas_id_binding")));
+ new Exception(MessageManager.getString(
+ "exception.overwriting_vamsas_id_binding")));
}
else if (jv2vobj.containsKey(jvobj)
&& !((VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))
{
- Cache.log
- .debug("Warning? Overwriting existing jalview object binding for "
+ Cache.log.debug(
+ "Warning? Overwriting existing jalview object binding for "
+ jvobj,
- new Exception(
- MessageManager
- .getString("exception.overwriting_jalview_id_binding")));
+ new Exception(MessageManager.getString(
+ "exception.overwriting_jalview_id_binding")));
}
/*
* Cache.log.error("Attempt to make conflicting object binding! "+vobj+" id "
{
throw new Error(MessageManager.formatMessage(
"error.implementation_error_old_jalview_object_not_bound",
- new String[] { oldjvobject.toString() }));
+ new String[]
+ { oldjvobject.toString() }));
}
if (newjvobject != null)
{
tojalview = true;
if (jvobj != null && !(boundType.isAssignableFrom(jvobj.getClass())))
{
- throw new Error(
- MessageManager
- .formatMessage(
- "error.implementation_error_vamsas_doc_class_should_bind_to_type",
- new String[] { vobj.getClass().toString(),
- boundType.toString(),
- jvobj.getClass().toString() }));
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_error_vamsas_doc_class_should_bind_to_type",
+ new String[]
+ { vobj.getClass().toString(), boundType.toString(),
+ jvobj.getClass().toString() }));
}
dsReg.registerDsObj(this);
}
vobj = getjv2vObj(jvobj);
if (vobj != null && !(boundToType.isAssignableFrom(vobj.getClass())))
{
- throw new Error(
- MessageManager
- .formatMessage(
- "error.implementation_error_vamsas_doc_class_should_bind_to_type",
- new String[] { jvobj2.getClass().toString(),
- boundToType.toString(),
- vobj.getClass().toString() }));
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_error_vamsas_doc_class_should_bind_to_type",
+ new String[]
+ { jvobj2.getClass().toString(), boundToType.toString(),
+ vobj.getClass().toString() }));
}
dsReg.registerDsObj(this);
}
jalview.datamodel.Provenance jprov = new jalview.datamodel.Provenance();
for (int i = 0; i < prov.getEntryCount(); i++)
{
- jprov.addEntry(prov.getEntry(i).getUser(), prov.getEntry(i)
- .getAction(), prov.getEntry(i).getDate(), prov.getEntry(i)
- .getId());
+ jprov.addEntry(prov.getEntry(i).getUser(),
+ prov.getEntry(i).getAction(), prov.getEntry(i).getDate(),
+ prov.getEntry(i).getId());
}
return jprov;
}
else
{
- jalview.bin.Cache.log.debug("Ignoring mapless DbRef.Map "
- + jvobj.getSrcAccString());
+ jalview.bin.Cache.log.debug(
+ "Ignoring mapless DbRef.Map " + jvobj.getSrcAccString());
}
}
*/
private void updateMapTo(jalview.datamodel.Mapping mp)
{
- log.info("Performing updateMapTo remove this message when we know what we're doing.");
+ log.info(
+ "Performing updateMapTo remove this message when we know what we're doing.");
// TODO determine how sequences associated with database mappings are stored
// in the document
if (mp != null && mp.getTo() != null)
// sync the dataset sequence, if it hasn't been done already.
// TODO: ensure real dataset sequence corresponding to getTo is
// recovered
- dssync = new Datasetsequence(
- datastore,
- mp.getTo(),
- (mp.getMappedWidth() == mp.getWidth()) ? sequence
- .getDictionary()
- : ((mp.getMappedWidth() == 3) ? uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA
+ dssync = new Datasetsequence(datastore, mp.getTo(),
+ (mp.getMappedWidth() == mp.getWidth())
+ ? sequence.getDictionary()
+ : ((mp.getMappedWidth() == 3)
+ ? uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA
: uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA),
ds);
}
{
DbRef vobj = (DbRef) this.vobj;
DBRefEntry jvobj = (DBRefEntry) this.jvobj;
- jalview.bin.Cache.log.debug("Conflict in dbentry update for "
- + vobj.getAccessionId() + vobj.getSource() + " "
- + vobj.getVorbaId());
+ jalview.bin.Cache.log
+ .debug("Conflict in dbentry update for " + vobj.getAccessionId()
+ + vobj.getSource() + " " + vobj.getVorbaId());
// TODO Auto-generated method stub
}
DbRef vobj = (DbRef) this.vobj;
DBRefEntry jvobj = (DBRefEntry) this.jvobj;
// add new dbref
- sq.addDBRef(jvobj = new jalview.datamodel.DBRefEntry(vobj.getSource()
- .toString(), vobj.getVersion().toString(), vobj
- .getAccessionId().toString()));
+ sq.addDBRef(jvobj = new jalview.datamodel.DBRefEntry(
+ vobj.getSource().toString(), vobj.getVersion().toString(),
+ vobj.getAccessionId().toString()));
if (vobj.getMapCount() > 0)
{
// TODO: Jalview ignores all the other maps
}
else
{
- jalview.bin.Cache.log.debug("Ignoring mapless DbRef.Map "
- + jvobj.getSrcAccString());
+ jalview.bin.Cache.log.debug(
+ "Ignoring mapless DbRef.Map " + jvobj.getSrcAccString());
}
}
}
super(datastore);
}
- public Rangetype(VamsasAppDatastore datastore, Vobject vobj, Class jvClass)
+ public Rangetype(VamsasAppDatastore datastore, Vobject vobj,
+ Class jvClass)
{
super(datastore, vobj, jvClass);
}
int[] se = null;
if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
{
- throw new Error(
- MessageManager
- .getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
+ throw new Error(MessageManager.getString(
+ "error.invalid_vamsas_rangetype_cannot_resolve_lists"));
}
if (dseta.getSegCount() > 0)
{
int[] se = null;
if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
{
- throw new Error(
- MessageManager
- .getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
+ throw new Error(MessageManager.getString(
+ "error.invalid_vamsas_rangetype_cannot_resolve_lists"));
}
if (dseta.getSegCount() > 0)
{
int[] se = null;
if (range.getSegCount() > 0 && range.getPosCount() > 0)
{
- throw new Error(
- MessageManager
- .getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
+ throw new Error(MessageManager.getString(
+ "error.invalid_vamsas_rangetype_cannot_resolve_lists"));
}
if (range.getSegCount() > 0)
{
* @param maprange
* where the from range is the local mapped range, and the to range
* is the 'mapped' range in the MapRangeType
- * @param default unit for local
- * @param default unit for mapped
+ * @param default
+ * unit for local
+ * @param default
+ * unit for mapped
* @return MapList
*/
protected jalview.util.MapList parsemapType(MapType maprange, int localu,
int[] mappedRange = getIntervals(maprange.getMapped());
long lu = maprange.getLocal().hasUnit() ? maprange.getLocal().getUnit()
: localu;
- long mu = maprange.getMapped().hasUnit() ? maprange.getMapped()
- .getUnit() : mappedu;
+ long mu = maprange.getMapped().hasUnit()
+ ? maprange.getMapped().getUnit()
+ : mappedu;
ml = new jalview.util.MapList(localRange, mappedRange, (int) lu,
(int) mu);
return ml;
{
if (ml == null)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_maplist_is_null"));
+ throw new Error(MessageManager
+ .getString("error.implementation_error_maplist_is_null"));
}
maprange.setLocal(new Local());
maprange.setMapped(new Mapped());
DataSetAnnotations dsa = (DataSetAnnotations) vobj;
if (dsa.getSeqRefCount() != 1)
{
- Cache.log
- .warn("Not binding "
- + dsa.getVorbaId()
- + " to Sequence Feature - has multiple dataset sequence references.");
+ Cache.log.warn("Not binding " + dsa.getVorbaId()
+ + " to Sequence Feature - has multiple dataset sequence references.");
return;
}
jalview.datamodel.SequenceFeature sf = (jalview.datamodel.SequenceFeature) jvobj;
if (dsa.getSeqRefCount() != 1)
{
replaceJvObjMapping(feature, null);
- Cache.log
- .warn("Binding of annotation to jalview feature has changed. Removing binding and recreating.");
+ Cache.log.warn(
+ "Binding of annotation to jalview feature has changed. Removing binding and recreating.");
doSync(); // re-verify bindings.
}
else
{
// conflicting update from document - we cannot map this feature anymore.
replaceJvObjMapping(feature, null);
- Cache.log
- .warn("annotation ("
- + dsa.getVorbaId()
- + " bound to jalview feature cannot be mapped. Removing binding, deleting feature, and deleting feature.");
+ Cache.log.warn("annotation (" + dsa.getVorbaId()
+ + " bound to jalview feature cannot be mapped. Removing binding, deleting feature, and deleting feature.");
// - consider deleting the feature ?
dsSeq.deleteFeature(feature);
// doSync();
vSeg.setInclusive(true);
if (dsa.getSegCount() > 1)
{
- Cache.log
- .debug("About to destroy complex annotation in vamsas document mapped to sequence feature ("
+ Cache.log.debug(
+ "About to destroy complex annotation in vamsas document mapped to sequence feature ("
+ dsa.getVorbaId() + ")");
}
dsa.setSeg(new Seg[] { vSeg });
else if (vlu instanceof Integer)
{
valid = true;
- nprop.setType(uk.ac.vamsas.objects.utils.Properties.INTEGERTYPE);
+ nprop.setType(
+ uk.ac.vamsas.objects.utils.Properties.INTEGERTYPE);
}
else if (vlu instanceof Float)
{
if (ds != null && sequenceMapping.is__stored_in_document()
&& sequenceMapping.getV_parent() != ds)
{
- jalview.bin.Cache.log
- .warn("Probable IMPLEMENTATION ERROR: "
- + ds
- + " doesn't match the parent of the bound sequence mapping object.");
+ jalview.bin.Cache.log.warn("Probable IMPLEMENTATION ERROR: " + ds
+ + " doesn't match the parent of the bound sequence mapping object.");
}
}
SequenceType to = (SequenceType) getjv2vObj(jvto);
if (to == null)
{
- jalview.bin.Cache.log
- .warn("FIXME NONFATAL - do a second update: Ignoring Forward Reference to seuqence not yet bound to vamsas seuqence object");
+ jalview.bin.Cache.log.warn(
+ "FIXME NONFATAL - do a second update: Ignoring Forward Reference to seuqence not yet bound to vamsas seuqence object");
return;
}
SequenceMapping sequenceMapping = new SequenceMapping();
if (!dnaToProt)
{
- jalview.bin.Cache.log
- .warn("Ignoring Mapping - don't support protein to protein mapping in vamsas document yet.");
+ jalview.bin.Cache.log.warn(
+ "Ignoring Mapping - don't support protein to protein mapping in vamsas document yet.");
return;
}
if (ds == null)
true);
}
ds.addSequenceMapping(sequenceMapping);
- sequenceMapping.setProvenance(this
- .dummyProvenance("user defined coding region translation")); // TODO:
+ sequenceMapping.setProvenance(
+ this.dummyProvenance("user defined coding region translation")); // TODO:
// correctly
// construct
// provenance
// mapping
bindjvvobj(mjvmapping.getMap(), sequenceMapping);
- jalview.bin.Cache.log.debug("Successfully created mapping "
- + sequenceMapping.getVorbaId());
+ jalview.bin.Cache.log.debug(
+ "Successfully created mapping " + sequenceMapping.getVorbaId());
}
// private void update(jalview.util.MapList mjvmapping,
private void update(jalview.datamodel.Mapping mjvmapping,
SequenceMapping sequenceMapping)
{
- jalview.bin.Cache.log
- .error("Not implemented: Jalview Update Sequence DBRef Mapping");
+ jalview.bin.Cache.log.error(
+ "Not implemented: Jalview Update Sequence DBRef Mapping");
}
/**
if (from == null || to == null)
{
- jalview.bin.Cache.log
- .error("Probable Vamsas implementation error : unbound dataset sequences involved in a mapping are being parsed!");
+ jalview.bin.Cache.log.error(
+ "Probable Vamsas implementation error : unbound dataset sequences involved in a mapping are being parsed!");
return;
}
boolean smaptolocal2tm = (tmpnnl) ? smap.equals(tmp.getMap())
: false;
// smap to maps from te.map to te.local
- boolean smaptotemap2local = (tmpnnl) ? smapI.equals(fmp
- .getMap()) : false;
+ boolean smaptotemap2local = (tmpnnl)
+ ? smapI.equals(fmp.getMap())
+ : false;
if (smapfromlocal2fe && smaptotemap2local)
{
// smap implies mapping from to to from
@Override
public void conflict()
{
- Cache.log
- .info("Update (with conflict) from vamsas document to alignment associated tree not implemented yet.");
+ Cache.log.info(
+ "Update (with conflict) from vamsas document to alignment associated tree not implemented yet.");
}
/*
else
{
// handle conflict
- log.info("TODO: Add the locally modified tree in Jalview as a new tree in document, leaving locked tree unchanged.");
+ log.info(
+ "TODO: Add the locally modified tree in Jalview as a new tree in document, leaving locked tree unchanged.");
}
}
// or just correctly resolve the tree's seqData to the correct alignment
// in
// the document.
- Vector alsqrefs = getjv2vObjs(findAlignmentSequences(jal, tp
- .getTree().getOriginalData().getSequences()));
+ Vector alsqrefs = getjv2vObjs(findAlignmentSequences(jal,
+ tp.getTree().getOriginalData().getSequences()));
Object[] alsqs = new Object[alsqrefs.size()];
alsqrefs.copyInto(alsqs);
vInput.setObjRef(alsqs);
* @return vector of alignment sequences in order of SeqCigar array (but
* missing unfound seqcigars)
*/
- private Vector findAlignmentSequences(AlignmentI jal, SeqCigar[] sequences)
+ private Vector findAlignmentSequences(AlignmentI jal,
+ SeqCigar[] sequences)
{
SeqCigar[] tseqs = new SeqCigar[sequences.length];
System.arraycopy(sequences, 0, tseqs, 0, sequences.length);
{
for (int t = 0; t < sequences.length; t++)
{
- if (tseqs[t] != null
- && (tseqs[t].getRefSeq() == asq || tseqs[t].getRefSeq() == asq
- .getDatasetSequence()))
+ if (tseqs[t] != null && (tseqs[t].getRefSeq() == asq
+ || tseqs[t].getRefSeq() == asq.getDatasetSequence()))
// && tseqs[t].getStart()>=asq.getStart() &&
// tseqs[t].getEnd()<=asq.getEnd())
{
}
if (alsq.size() < sequences.length)
{
- Cache.log
- .warn("Not recovered all alignment sequences for given set of input sequence CIGARS");
+ Cache.log.warn(
+ "Not recovered all alignment sequences for given set of input sequence CIGARS");
}
return alsq;
}
if (tp.getTree() == null)
{
- Cache.log.warn("Not updating SequenceTreeMap for "
- + tree.getVorbaId());
+ Cache.log.warn(
+ "Not updating SequenceTreeMap for " + tree.getVorbaId());
return;
}
- Vector<SequenceNode> leaves = tp.getTree().findLeaves(
- tp.getTree().getTopNode());
+ Vector<SequenceNode> leaves = tp.getTree()
+ .findLeaves(tp.getTree().getTopNode());
Treenode[] tn = tree.getTreenode(); // todo: select nodes for this
// particular tree
int sz = tn.length;
else
{
leaf.setPlaceholder(true);
- leaf.setElement(new Sequence(leaf.getName(), "THISISAPLACEHLDER"));
+ leaf.setElement(
+ new Sequence(leaf.getName(), "THISISAPLACEHLDER"));
}
}
}
*/
public Treenode[] makeTreeNodes(TreeModel treeModel, Newick newick)
{
- Vector<SequenceNode> leaves = treeModel.findLeaves(treeModel
- .getTopNode());
+ Vector<SequenceNode> leaves = treeModel
+ .findLeaves(treeModel.getTopNode());
Vector tnv = new Vector();
Enumeration l = leaves.elements();
Hashtable nodespecs = new Hashtable();
else
{
System.err.println("WARNING: Unassociated treeNode "
- + tnode.element().toString()
- + " "
- + ((tnode.getName() != null) ? " label "
- + tnode.getName() : ""));
+ + tnode.element().toString() + " "
+ + ((tnode.getName() != null)
+ ? " label " + tnode.getName()
+ : ""));
}
}
}
{
if (tp.getEntry(pe).getInputCount() > 1)
{
- Cache.log
- .warn("Ignoring additional input spec in provenance entry "
+ Cache.log.warn(
+ "Ignoring additional input spec in provenance entry "
+ tp.getEntry(pe).toString());
}
// LATER: deal sensibly with multiple inputs
// is this the whole alignment or a specific set of sequences ?
if (vInput.getObjRefCount() == 0)
{
- if (tree.getV_parent() != null
- && tree.getV_parent() instanceof uk.ac.vamsas.objects.core.Alignment)
+ if (tree.getV_parent() != null && tree
+ .getV_parent() instanceof uk.ac.vamsas.objects.core.Alignment)
{
javport = getViewport(tree.getV_parent());
jal = javport.getAlignment();
else
{
// Explicit reference - to alignment, sequences or what.
- if (vInput.getObjRefCount() == 1
- && vInput.getObjRef(0) instanceof uk.ac.vamsas.objects.core.Alignment)
+ if (vInput.getObjRefCount() == 1 && vInput.getObjRef(
+ 0) instanceof uk.ac.vamsas.objects.core.Alignment)
{
// recover an AlignmentView for the input data
javport = getViewport((Vobject) vInput.getObjRef(0));
jal = javport.getAlignment();
view = javport.getAlignment().getCompactAlignment();
}
- else if (vInput.getObjRef(0) instanceof uk.ac.vamsas.objects.core.AlignmentSequence)
+ else if (vInput.getObjRef(
+ 0) instanceof uk.ac.vamsas.objects.core.AlignmentSequence)
{
// recover an AlignmentView for the input data
- javport = getViewport(((Vobject) vInput.getObjRef(0))
- .getV_parent());
+ javport = getViewport(
+ ((Vobject) vInput.getObjRef(0)).getV_parent());
jal = javport.getAlignment();
jalview.datamodel.SequenceI[] seqs = new jalview.datamodel.SequenceI[vInput
.getObjRefCount()];
for (int i = 0, iSize = vInput.getObjRefCount(); i < iSize; i++)
{
- SequenceI seq = (SequenceI) getvObj2jv((Vobject) vInput
- .getObjRef(i));
+ SequenceI seq = (SequenceI) getvObj2jv(
+ (Vobject) vInput.getObjRef(i));
seqs[i] = seq;
}
view = new jalview.datamodel.Alignment(seqs)
return new Object[] { new AlignmentView(view), jal };
}
}
- Cache.log
- .debug("Returning null for input data recovery from provenance.");
+ Cache.log.debug(
+ "Returning null for input data recovery from provenance.");
return null;
}
{
System.err.println("Falling back to javascript: url call");
}
- StringBuffer sb = new StringBuffer("javascript:" + _listener
- + "(");
+ StringBuffer sb = new StringBuffer(
+ "javascript:" + _listener + "(");
for (int i = 0; objects != null && i < objects.length; i++)
{
if (i > 0)
sb.append("\"");
// strip out nulls and complex objects that we can't pass this
// way.
- if (objects[i] != null
- && !(objects[i].getClass().getName()
- .indexOf("jalview") == 0))
+ if (objects[i] != null && !(objects[i].getClass().getName()
+ .indexOf("jalview") == 0))
{
sb.append(objects[i].toString());
}
* @return String list of selected sequence IDs, each terminated by the given
* separator
*/
- public abstract String getSelectedSequencesFrom(AlignFrame alf, String sep);
+ public abstract String getSelectedSequencesFrom(AlignFrame alf,
+ String sep);
/**
*
* @param sep
* separator between toselect fields
*/
- public abstract void select(String sequenceIds, String columns, String sep);
+ public abstract void select(String sequenceIds, String columns,
+ String sep);
/**
* select regions of the given alignment frame
* @return selected sequences as flat file or empty string if there was no
* current selection
*/
- public abstract String getSelectedSequencesAsAlignmentFrom(
- AlignFrame alf, String format, String suffix);
+ public abstract String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
+ String format, String suffix);
/**
* get a separator separated list of sequence IDs reflecting the order of the
* @param alf
* @param annotation
*/
- public abstract void loadAnnotationFrom(AlignFrame alf, String annotation);
+ public abstract void loadAnnotationFrom(AlignFrame alf,
+ String annotation);
/**
* parse the given string as a jalview feature or GFF annotation file and
* Jmol (e.g. first one is frame 1, second is frame 2, etc).
* @see jalview.javascript.MouseOverStructureListener
*/
- public abstract void setStructureListener(String listener, String modelSet);
+ public abstract void setStructureListener(String listener,
+ String modelSet);
/**
* remove any callback using the given listener function and associated with
* @see jalview.appletgui.AlignFrame#setFeatureGroupState(java.lang.String[],
* boolean)
*/
- public abstract void setFeatureGroupStateOn(AlignFrame alf,
- String groups, boolean state);
+ public abstract void setFeatureGroupStateOn(AlignFrame alf, String groups,
+ boolean state);
public abstract void setFeatureGroupState(String groups, boolean state);
import jalview.datamodel.SequenceGroup;
import jalview.structure.SelectionSource;
-public class JsSelectionSender extends JSFunctionExec implements
- jalview.structure.SelectionListener, JsCallBack
+public class JsSelectionSender extends JSFunctionExec
+ implements jalview.structure.SelectionListener, JsCallBack
{
AlignFrame _af;
public void selection(SequenceGroup seqsel, ColumnSelection colsel,
HiddenColumns hidden, SelectionSource source)
{
- // System.err.println("Testing selection event relay to jsfunction:"+_listener);
+ // System.err.println("Testing selection event relay to
+ // jsfunction:"+_listener);
try
{
String setid = "";
}
String[] seqs = new String[] {};
String[] cols = new String[] {};
- int strt = 0, end = (src == null) ? -1 : src.alignPanel.av
- .getAlignment().getWidth();
+ int strt = 0, end = (src == null) ? -1
+ : src.alignPanel.av.getAlignment().getWidth();
if (seqsel != null && seqsel.getSize() > 0)
{
seqs = new String[seqsel.getSize()];
}
System.err.println("Relaying selection to jsfunction:" + _listener);
executeJavascriptFunction(_listener,
- new Object[] { src, setid, jvlite.arrayToSeparatorList(seqs),
+ new Object[]
+ { src, setid, jvlite.arrayToSeparatorList(seqs),
jvlite.arrayToSeparatorList(cols) });
} catch (Exception ex)
{
- System.err
- .println("Jalview Javascript exec error: Couldn't send selection message using function '"
+ System.err.println(
+ "Jalview Javascript exec error: Couldn't send selection message using function '"
+ _listener + "'");
ex.printStackTrace();
if (ex instanceof netscape.javascript.JSException)
import jalview.structure.VamsasListener;
import jalview.structure.VamsasSource;
-public class MouseOverListener extends JSFunctionExec implements
- VamsasListener, JsCallBack
+public class MouseOverListener extends JSFunctionExec
+ implements VamsasListener, JsCallBack
{
AlignFrame _af;
// function
}
executeJavascriptFunction(_listener,
- new Object[] { src, seq.getDisplayId(false), "" + (1 + i),
+ new Object[]
+ { src, seq.getDisplayId(false), "" + (1 + i),
"" + seq.findPosition(i) });
} catch (Exception ex)
{
- System.err
- .println("JalviewLite javascript error: Couldn't send mouseOver with handler '"
+ System.err.println(
+ "JalviewLite javascript error: Couldn't send mouseOver with handler '"
+ _listener + "'");
if (ex instanceof netscape.javascript.JSException)
{
* @author Jim Procter (jprocter)
*
*/
-public class MouseOverStructureListener extends JSFunctionExec implements
- JsCallBack, StructureListener
+public class MouseOverStructureListener extends JSFunctionExec
+ implements JsCallBack, StructureListener
{
String _listenerfn;
// JBPComment: yep - this is right! the Javascript harness uses the
// absolute pdbFile URI to locate the PDB file in the external viewer
executeJavascriptFunction(_listenerfn,
- new String[] { "mouseover", "" + atom.getPdbFile(),
- "" + atom.getChain(), "" + (atom.getPdbResNum()),
- "" + atom.getAtomIndex() });
+ new String[]
+ { "mouseover", "" + atom.getPdbFile(), "" + atom.getChain(),
+ "" + (atom.getPdbResNum()), "" + atom.getAtomIndex() });
} catch (Exception ex)
{
System.err.println("Couldn't execute callback with " + _listenerfn
if (JalviewLite.debug)
{
- System.err.println(this.getClass().getName() + " modelSet[0]: "
- + modelSet[0]);
+ System.err.println(
+ this.getClass().getName() + " modelSet[0]: " + modelSet[0]);
ssm.reportMapping();
}
SequenceRenderer sr = ((jalview.appletgui.AlignmentPanel) source)
.getSequenceRenderer();
FeatureRenderer fr = ((jalview.appletgui.AlignmentPanel) source).av
- .isShowSequenceFeatures() ? new jalview.appletgui.FeatureRenderer(
- ((jalview.appletgui.AlignmentPanel) source).av) : null;
+ .isShowSequenceFeatures()
+ ? new jalview.appletgui.FeatureRenderer(
+ ((jalview.appletgui.AlignmentPanel) source).av)
+ : null;
if (fr != null)
{
- ((jalview.appletgui.FeatureRenderer) fr)
- .transferSettings(((jalview.appletgui.AlignmentPanel) source)
+ ((jalview.appletgui.FeatureRenderer) fr).transferSettings(
+ ((jalview.appletgui.AlignmentPanel) source)
.getFeatureRenderer());
}
;
System.arraycopy(ccset, 0, ccomandset, sz, ccset.length);
sz += ccset.length;
}
- if (jvlite.isJsMessageSetChanged(
- mclass = "colourstruct",
+ if (jvlite.isJsMessageSetChanged(mclass = "colourstruct",
mhandle = ((jalview.appletgui.AlignmentPanel) source).av
- .getViewId(), ccomandset))
+ .getViewId(),
+ ccomandset))
{
jvlite.setJsMessageSet(mclass, mhandle, ccomandset);
// and notify javascript handler
- String st[] = new String[] {
- "colourstruct",
+ String st[] = new String[] { "colourstruct",
"" + ((jalview.appletgui.AlignmentPanel) source).av.getViewId(),
- "" + ccomandset.length,
- jvlite.arrayToSeparatorList(pdbfn.toArray(new String[pdbfn
- .size()])) };
+ "" + ccomandset.length, jvlite.arrayToSeparatorList(
+ pdbfn.toArray(new String[pdbfn.size()])) };
try
{
executeJavascriptFunction(true, _listenerfn, st);
} catch (Exception ex)
{
- System.err.println("Couldn't execute callback with "
- + _listenerfn + " using args { " + st[0] + ", " + st[1]
- + ", " + st[2] + "," + st[3] + "}"); // + ","+st[4]+"\n");
+ System.err.println("Couldn't execute callback with " + _listenerfn
+ + " using args { " + st[0] + ", " + st[1] + ", " + st[2]
+ + "," + st[3] + "}"); // + ","+st[4]+"\n");
ex.printStackTrace();
}
public void init()
{
- chkHiddenSeqs.setText(MessageManager
- .getString("action.export_hidden_sequences"));
- chkHiddenCols.setText(MessageManager
- .getString("action.export_hidden_columns"));
- chkExportAnnots.setText(MessageManager
- .getString("action.export_annotations"));
- chkExportFeats.setText(MessageManager
- .getString("action.export_features"));
+ chkHiddenSeqs.setText(
+ MessageManager.getString("action.export_hidden_sequences"));
+ chkHiddenCols.setText(
+ MessageManager.getString("action.export_hidden_columns"));
+ chkExportAnnots
+ .setText(MessageManager.getString("action.export_annotations"));
+ chkExportFeats
+ .setText(MessageManager.getString("action.export_features"));
chkExportGrps.setText(MessageManager.getString("action.export_groups"));
btnOk.setText(MessageManager.getString("action.ok"));
btnCancel.setText(MessageManager.getString("action.cancel"));
chkHiddenCols.setSelected(chkHiddenCols.isEnabled() && isSelected);
chkExportAnnots.setSelected(isComplexAlignFile
&& chkExportAnnots.isEnabled() && isSelected);
- chkExportFeats.setSelected(isComplexAlignFile
- && chkExportFeats.isEnabled() && isSelected);
- chkExportGrps.setSelected(isComplexAlignFile
- && chkExportGrps.isEnabled() && isSelected);
+ chkExportFeats.setSelected(
+ isComplexAlignFile && chkExportFeats.isEnabled() && isSelected);
+ chkExportGrps.setSelected(
+ isComplexAlignFile && chkExportGrps.isEnabled() && isSelected);
}
public boolean isShowDialog()
};
// FIXME getDefaultToolkit throws an exception in Headless mode
- KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask()
- | KeyEvent.SHIFT_MASK, false);
+ KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.SHIFT_MASK,
+ false);
addMenuActionAndAccelerator(keyStroke, saveAs, al);
closeMenuItem.setText(MessageManager.getString("action.close"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
webService.setText(MessageManager.getString("action.web_service"));
JMenuItem selectAllSequenceMenuItem = new JMenuItem(
MessageManager.getString("action.select_all"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
JMenuItem invertSequenceMenuItem = new JMenuItem(
MessageManager.getString("action.invert_sequence_selection"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
});
JMenuItem expandAlignment = new JMenuItem(
MessageManager.getString("action.view_flanking_regions"));
- expandAlignment.setToolTipText(MessageManager
- .getString("label.view_flanking_regions"));
+ expandAlignment.setToolTipText(
+ MessageManager.getString("label.view_flanking_regions"));
expandAlignment.addActionListener(new ActionListener()
{
@Override
});
JMenuItem remove2LeftMenuItem = new JMenuItem(
MessageManager.getString("action.remove_left"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
JMenuItem remove2RightMenuItem = new JMenuItem(
MessageManager.getString("action.remove_right"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
JMenuItem removeGappedColumnMenuItem = new JMenuItem(
MessageManager.getString("action.remove_empty_columns"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
JMenuItem removeAllGapsMenuItem = new JMenuItem(
MessageManager.getString("action.remove_all_gaps"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask()
- | KeyEvent.SHIFT_MASK, false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.SHIFT_MASK,
+ false);
al = new ActionListener()
{
@Override
viewTextMenuItem_actionPerformed(e);
}
});
- showNonconservedMenuItem.setText(MessageManager
- .getString("label.show_non_conserved"));
+ showNonconservedMenuItem
+ .setText(MessageManager.getString("label.show_non_conserved"));
showNonconservedMenuItem.setState(false);
showNonconservedMenuItem.addActionListener(new ActionListener()
{
JMenuItem removeRedundancyMenuItem = new JMenuItem(
MessageManager.getString("action.remove_redundancy"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
statusBar.setText(MessageManager.getString("label.status_bar"));
- outputTextboxMenu.setText(MessageManager
- .getString("label.out_to_textbox"));
+ outputTextboxMenu
+ .setText(MessageManager.getString("label.out_to_textbox"));
annotationPanelMenuItem.setActionCommand("");
- annotationPanelMenuItem.setText(MessageManager
- .getString("label.show_annotations"));
- annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
- true));
+ annotationPanelMenuItem
+ .setText(MessageManager.getString("label.show_annotations"));
+ annotationPanelMenuItem
+ .setState(Cache.getDefault("SHOW_ANNOTATIONS", true));
annotationPanelMenuItem.addActionListener(new ActionListener()
{
@Override
annotationPanelMenuItem_actionPerformed(e);
}
});
- showAllAlAnnotations.setText(MessageManager
- .getString("label.show_all_al_annotations"));
+ showAllAlAnnotations.setText(
+ MessageManager.getString("label.show_all_al_annotations"));
final boolean isAnnotationPanelShown = annotationPanelMenuItem
.getState();
showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
showAllAnnotations_actionPerformed(false, true);
}
});
- hideAllAlAnnotations.setText(MessageManager
- .getString("label.hide_all_al_annotations"));
+ hideAllAlAnnotations.setText(
+ MessageManager.getString("label.hide_all_al_annotations"));
hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
hideAllAlAnnotations.addActionListener(new ActionListener()
{
hideAllAnnotations_actionPerformed(false, true);
}
});
- showAllSeqAnnotations.setText(MessageManager
- .getString("label.show_all_seq_annotations"));
+ showAllSeqAnnotations.setText(
+ MessageManager.getString("label.show_all_seq_annotations"));
showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
showAllSeqAnnotations.addActionListener(new ActionListener()
{
showAllAnnotations_actionPerformed(true, false);
}
});
- hideAllSeqAnnotations.setText(MessageManager
- .getString("label.hide_all_seq_annotations"));
+ hideAllSeqAnnotations.setText(
+ MessageManager.getString("label.hide_all_seq_annotations"));
hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
hideAllSeqAnnotations.addActionListener(new ActionListener()
{
final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
MessageManager.getString("label.sort_annotations_by_label"));
- sortAnnBySequence
- .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
+ sortAnnBySequence.setSelected(
+ sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
sortAnnBySequence.addActionListener(new ActionListener()
{
@Override
{
boolean newState = sortAnnBySequence.getState();
sortAnnByLabel.setSelected(false);
- setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
- : SequenceAnnotationOrder.NONE);
+ setAnnotationSortOrder(
+ newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
+ : SequenceAnnotationOrder.NONE);
sortAnnotations_actionPerformed();
}
});
- sortAnnByLabel
- .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
+ sortAnnByLabel.setSelected(
+ sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
sortAnnByLabel.addActionListener(new ActionListener()
{
@Override
{
boolean newState = sortAnnByLabel.getState();
sortAnnBySequence.setSelected(false);
- setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
- : SequenceAnnotationOrder.NONE);
+ setAnnotationSortOrder(
+ newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
+ : SequenceAnnotationOrder.NONE);
sortAnnotations_actionPerformed();
}
});
colourTextMenuItem = new JCheckBoxMenuItem(
- MessageManager
- .getString("label.colour_text"));
+ MessageManager.getString("label.colour_text"));
colourTextMenuItem.addActionListener(new ActionListener()
{
@Override
undoMenuItem.setEnabled(false);
undoMenuItem.setText(MessageManager.getString("action.undo"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
redoMenuItem.setEnabled(false);
redoMenuItem.setText(MessageManager.getString("action.redo"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
JMenuItem printMenuItem = new JMenuItem(
MessageManager.getString("action.print"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
JMenuItem findMenuItem = new JMenuItem(
MessageManager.getString("action.find"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
MessageManager.getString("label.find_tip")));
al = new ActionListener()
};
addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
- showSeqFeatures.setText(MessageManager
- .getString("label.show_sequence_features"));
+ showSeqFeatures.setText(
+ MessageManager.getString("label.show_sequence_features"));
showSeqFeatures.addActionListener(new ActionListener()
{
@Override
* void actionPerformed(ActionEvent actionEvent) {
* showSeqFeaturesHeight_actionPerformed(actionEvent); } });
*/
- showDbRefsMenuitem.setText(MessageManager
- .getString("label.show_database_refs"));
+ showDbRefsMenuitem
+ .setText(MessageManager.getString("label.show_database_refs"));
showDbRefsMenuitem.addActionListener(new ActionListener()
{
}
});
- showNpFeatsMenuitem.setText(MessageManager
- .getString("label.show_non_positional_features"));
+ showNpFeatsMenuitem.setText(
+ MessageManager.getString("label.show_non_positional_features"));
showNpFeatsMenuitem.addActionListener(new ActionListener()
{
}
});
- showGroupConservation.setText(MessageManager
- .getString("label.group_conservation"));
+ showGroupConservation
+ .setText(MessageManager.getString("label.group_conservation"));
showGroupConservation.addActionListener(new ActionListener()
{
});
- showGroupConsensus.setText(MessageManager
- .getString("label.group_consensus"));
+ showGroupConsensus
+ .setText(MessageManager.getString("label.group_consensus"));
showGroupConsensus.addActionListener(new ActionListener()
{
}
});
- showConsensusHistogram.setText(MessageManager
- .getString("label.show_consensus_histogram"));
+ showConsensusHistogram.setText(
+ MessageManager.getString("label.show_consensus_histogram"));
showConsensusHistogram.addActionListener(new ActionListener()
{
}
});
- showSequenceLogo.setText(MessageManager
- .getString("label.show_consensus_logo"));
+ showSequenceLogo
+ .setText(MessageManager.getString("label.show_consensus_logo"));
showSequenceLogo.addActionListener(new ActionListener()
{
}
});
- normaliseSequenceLogo.setText(MessageManager
- .getString("label.norm_consensus_logo"));
+ normaliseSequenceLogo
+ .setText(MessageManager.getString("label.norm_consensus_logo"));
normaliseSequenceLogo.addActionListener(new ActionListener()
{
}
});
- applyAutoAnnotationSettings.setText(MessageManager
- .getString("label.apply_all_groups"));
+ applyAutoAnnotationSettings
+ .setText(MessageManager.getString("label.apply_all_groups"));
applyAutoAnnotationSettings.setState(false);
applyAutoAnnotationSettings.setVisible(true);
applyAutoAnnotationSettings.addActionListener(new ActionListener()
MessageManager.getString("label.show_last"));
buttonGroup.add(showAutoFirst);
buttonGroup.add(showAutoLast);
- final boolean autoFirst = Cache.getDefault(
- Preferences.SHOW_AUTOCALC_ABOVE, false);
+ final boolean autoFirst = Cache
+ .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
showAutoFirst.setSelected(autoFirst);
setShowAutoCalculatedAbove(autoFirst);
showAutoFirst.addActionListener(new ActionListener()
JMenuItem deleteGroups = new JMenuItem(
MessageManager.getString("action.undefine_groups"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
JMenuItem createGroup = new JMenuItem(
MessageManager.getString("action.create_group"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
JMenuItem unGroup = new JMenuItem(
MessageManager.getString("action.remove_group"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask()
- | KeyEvent.SHIFT_MASK, false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.SHIFT_MASK,
+ false);
al = new ActionListener()
{
@Override
addMenuActionAndAccelerator(keyStroke, unGroup, al);
copy.setText(MessageManager.getString("action.copy"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
addMenuActionAndAccelerator(keyStroke, copy, al);
cut.setText(MessageManager.getString("action.cut"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
pasteMenu.setText(MessageManager.getString("action.paste"));
JMenuItem pasteNew = new JMenuItem(
MessageManager.getString("label.to_new_alignment"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask()
- | KeyEvent.SHIFT_MASK, false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.SHIFT_MASK,
+ false);
al = new ActionListener()
{
@Override
JMenuItem pasteThis = new JMenuItem(
MessageManager.getString("label.to_this_alignment"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
createPNG(null);
}
});
- createPNG.setActionCommand(MessageManager
- .getString("label.save_png_image"));
+ createPNG.setActionCommand(
+ MessageManager.getString("label.save_png_image"));
JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
font.addActionListener(new ActionListener()
font_actionPerformed(e);
}
});
- seqLimits.setText(MessageManager
- .getString("label.show_sequence_limits"));
+ seqLimits.setText(
+ MessageManager.getString("label.show_sequence_limits"));
seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
seqLimits.addActionListener(new ActionListener()
{
JMenuItem loadTreeMenuItem = new JMenuItem(
MessageManager.getString("label.load_associated_tree"));
- loadTreeMenuItem.setActionCommand(MessageManager
- .getString("label.load_tree_for_sequence_set"));
+ loadTreeMenuItem.setActionCommand(
+ MessageManager.getString("label.load_tree_for_sequence_set"));
loadTreeMenuItem.addActionListener(new ActionListener()
{
@Override
});
centreColumnLabelsMenuItem.setVisible(true);
centreColumnLabelsMenuItem.setState(false);
- centreColumnLabelsMenuItem.setText(MessageManager
- .getString("label.centre_column_labels"));
+ centreColumnLabelsMenuItem.setText(
+ MessageManager.getString("label.centre_column_labels"));
centreColumnLabelsMenuItem.addActionListener(new ActionListener()
{
@Override
});
followHighlightMenuItem.setVisible(true);
followHighlightMenuItem.setState(true);
- followHighlightMenuItem.setText(MessageManager
- .getString("label.automatic_scrolling"));
+ followHighlightMenuItem
+ .setText(MessageManager.getString("label.automatic_scrolling"));
followHighlightMenuItem.addActionListener(new ActionListener()
{
{
}
});
- sortByAnnotScore.setText(MessageManager
- .getString("label.sort_by_score"));
+ sortByAnnotScore
+ .setText(MessageManager.getString("label.sort_by_score"));
sort.add(sortByAnnotScore);
sort.addMenuListener(new javax.swing.event.MenuListener()
{
});
sortByAnnotScore.setVisible(false);
- calculateTree.setText(MessageManager
- .getString("action.calculate_tree_pca"));
+ calculateTree
+ .setText(MessageManager.getString("action.calculate_tree_pca"));
padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
- padGapsMenuitem.setState(jalview.bin.Cache
- .getDefault("PAD_GAPS", false));
+ padGapsMenuitem
+ .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
padGapsMenuitem.addActionListener(new ActionListener()
{
@Override
vamsasStore_actionPerformed(e);
}
});
- showTranslation.setText(MessageManager
- .getString("label.translate_cDNA"));
+ showTranslation
+ .setText(MessageManager.getString("label.translate_cDNA"));
showTranslation.addActionListener(new ActionListener()
{
@Override
showReverse_actionPerformed(false);
}
});
- showReverseComplement.setText(MessageManager
- .getString("label.reverse_complement"));
+ showReverseComplement
+ .setText(MessageManager.getString("label.reverse_complement"));
showReverseComplement.addActionListener(new ActionListener()
{
@Override
showProducts.setText(MessageManager.getString("label.get_cross_refs"));
runGroovy.setText(MessageManager.getString("label.run_groovy"));
- runGroovy.setToolTipText(MessageManager
- .getString("label.run_groovy_tip"));
+ runGroovy.setToolTipText(
+ MessageManager.getString("label.run_groovy_tip"));
runGroovy.addActionListener(new ActionListener()
{
@Override
associatedData_actionPerformed(e);
}
});
- autoCalculate.setText(MessageManager
- .getString("label.autocalculate_consensus"));
- autoCalculate.setState(jalview.bin.Cache.getDefault(
- "AUTO_CALC_CONSENSUS", true));
+ autoCalculate.setText(
+ MessageManager.getString("label.autocalculate_consensus"));
+ autoCalculate.setState(
+ jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
autoCalculate.addActionListener(new ActionListener()
{
@Override
autoCalculate_actionPerformed(e);
}
});
- sortByTree.setText(MessageManager
- .getString("label.sort_alignment_new_tree"));
- sortByTree
- .setToolTipText("<html>"
- + MessageManager
- .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
+ sortByTree.setText(
+ MessageManager.getString("label.sort_alignment_new_tree"));
+ sortByTree.setToolTipText("<html>" + MessageManager.getString(
+ "label.enable_automatically_sort_alignment_when_open_new_tree"));
sortByTree
.setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
sortByTree.addActionListener(new ActionListener()
}
});
- listenToViewSelections.setText(MessageManager
- .getString("label.listen_for_selections"));
+ listenToViewSelections.setText(
+ MessageManager.getString("label.listen_for_selections"));
listenToViewSelections
- .setToolTipText("<html>"
- + MessageManager
- .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
+ .setToolTipText("<html>" + MessageManager.getString(
+ "label.selections_mirror_selections_made_same_sequences_other_views"));
listenToViewSelections.setState(false);
listenToViewSelections.addActionListener(new ActionListener()
{
statusPanel.setLayout(new GridLayout());
JMenuItem showAllSeqs = new JMenuItem(
MessageManager.getString("label.all_sequences"));
- showAllSeqs.setToolTipText(MessageManager
- .getString("label.toggle_sequence_visibility"));
+ showAllSeqs.setToolTipText(
+ MessageManager.getString("label.toggle_sequence_visibility"));
showAllSeqs.addActionListener(new ActionListener()
{
@Override
});
JMenuItem showAllColumns = new JMenuItem(
MessageManager.getString("label.all_columns"));
- showAllColumns.setToolTipText(MessageManager
- .getString("label.toggle_columns_visibility"));
+ showAllColumns.setToolTipText(
+ MessageManager.getString("label.toggle_columns_visibility"));
showAllColumns.addActionListener(new ActionListener()
{
@Override
JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
JMenuItem hideSelSequences = new JMenuItem(
MessageManager.getString("label.selected_sequences"));
- hideSelSequences.setToolTipText(MessageManager
- .getString("label.toggle_sequence_visibility"));
+ hideSelSequences.setToolTipText(
+ MessageManager.getString("label.toggle_sequence_visibility"));
hideSelSequences.addActionListener(new ActionListener()
{
@Override
});
JMenuItem hideSelColumns = new JMenuItem(
MessageManager.getString("label.selected_columns"));
- hideSelColumns.setToolTipText(MessageManager
- .getString("label.toggle_columns_visibility"));
+ hideSelColumns.setToolTipText(
+ MessageManager.getString("label.toggle_columns_visibility"));
hideSelColumns.addActionListener(new ActionListener()
{
@Override
showAllhidden_actionPerformed(e);
}
});
- hiddenMarkers.setText(MessageManager
- .getString("action.show_hidden_markers"));
+ hiddenMarkers.setText(
+ MessageManager.getString("action.show_hidden_markers"));
hiddenMarkers.addActionListener(new ActionListener()
{
@Override
JMenuItem invertColSel = new JMenuItem(
MessageManager.getString("action.invert_column_selection"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask()
- | KeyEvent.ALT_MASK, false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.ALT_MASK,
+ false);
al = new ActionListener()
{
@Override
});
JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
JMenuItem newView = new JMenuItem(
MessageManager.getString("action.new_view"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
{
@Override
formatMenu.setText(MessageManager.getString("action.format"));
JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
- idRightAlign.setText(MessageManager
- .getString("label.right_align_sequence_id"));
+ idRightAlign.setText(
+ MessageManager.getString("label.right_align_sequence_id"));
idRightAlign.addActionListener(new ActionListener()
{
@Override
});
JMenuItem selectHighlighted = new JMenuItem(
MessageManager.getString("action.select_highlighted_columns"));
- selectHighlighted.setToolTipText(MessageManager
- .getString("tooltip.select_highlighted_columns"));
+ selectHighlighted.setToolTipText(
+ MessageManager.getString("tooltip.select_highlighted_columns"));
al = new ActionListener()
{
@Override
autoAnnMenu.add(showGroupConsensus);
annotationsMenu.add(autoAnnMenu);
-
sort.add(sortIDMenuItem);
sort.add(sortLengthMenuItem);
sort.add(sortGroupMenuItem);
@Override
public void actionPerformed(ActionEvent e)
{
- conservationMenuItem_actionPerformed(conservationMenuItem
- .isSelected());
+ conservationMenuItem_actionPerformed(
+ conservationMenuItem.isSelected());
}
});
modifyPID_actionPerformed();
}
});
- modifyConservation = new JMenuItem(
- MessageManager
+ modifyConservation = new JMenuItem(MessageManager
.getString("label.modify_conservation_threshold"));
modifyConservation.addActionListener(new ActionListener()
{
}
});
close.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
+ java.awt.event.KeyEvent.VK_W,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
selectAll.setText(MessageManager.getString("action.select_all"));
selectAll.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_A, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
+ java.awt.event.KeyEvent.VK_A,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
selectAll.addActionListener(new ActionListener()
{
@Override
jMenu1.setText(MessageManager.getString("action.file"));
save.setText(MessageManager.getString("action.save"));
save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
+ java.awt.event.KeyEvent.VK_S,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
save.addActionListener(new ActionListener()
{
@Override
}
});
copyItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
+ java.awt.event.KeyEvent.VK_C,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
editMenubar.add(jMenu1);
editMenubar.add(editMenu);
copyItem_actionPerformed(e);
}
});
- displaySource.setText(MessageManager
- .getString("action.show_html_source"));
- displaySource.setToolTipText(MessageManager
- .getString("label.select_copy_raw_html"));
+ displaySource
+ .setText(MessageManager.getString("action.show_html_source"));
+ displaySource.setToolTipText(
+ MessageManager.getString("label.select_copy_raw_html"));
displaySource.addActionListener(new ActionListener()
{
selectAll.setText(MessageManager.getString("action.select_all"));
selectAll.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_A, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
+ java.awt.event.KeyEvent.VK_A,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
selectAll.addActionListener(new ActionListener()
{
@Override
jMenu1.setText(MessageManager.getString("action.file"));
save.setText(MessageManager.getString("action.save"));
save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
+ java.awt.event.KeyEvent.VK_S,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
save.addActionListener(new ActionListener()
{
@Override
}
});
copyItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
+ java.awt.event.KeyEvent.VK_C,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
pasteMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
- .getMenuShortcutKeyMask(), false));
+ java.awt.event.KeyEvent.VK_V,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
editMenubar.add(jMenu1);
editMenubar.add(editMenu);
textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 12));
private void jbInit() throws Exception
{
this.setLayout(gridBagLayout1);
- refresh.setText(MessageManager
- .getString("label.refresh_available_sources"));
+ refresh.setText(
+ MessageManager.getString("label.refresh_available_sources"));
refresh.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
this.add(jPanel1, new GridBagConstraints(0, 3, 3, 1, 1.0, 1.0,
GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
new Insets(0, 0, 0, 0), 0, 0));
- this.add(fullDetailsScrollpane, new GridBagConstraints(1, 0, 2, 1, 1.0,
- 1.0, GridBagConstraints.CENTER, GridBagConstraints.BOTH,
- new Insets(3, 0, 0, 3), 240, 130));
- this.add(scrollPane, new GridBagConstraints(0, 0, 1, 1, 1.0, 1.0,
- GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
- 3, 2, 0, 0), 150, 130));
+ this.add(fullDetailsScrollpane,
+ new GridBagConstraints(1, 0, 2, 1, 1.0, 1.0,
+ GridBagConstraints.CENTER, GridBagConstraints.BOTH,
+ new Insets(3, 0, 0, 3), 240, 130));
+ this.add(scrollPane,
+ new GridBagConstraints(0, 0, 1, 1, 1.0, 1.0,
+ GridBagConstraints.CENTER, GridBagConstraints.BOTH,
+ new Insets(3, 2, 0, 0), 150, 130));
jPanel2.add(registryLabel, java.awt.BorderLayout.WEST);
jPanel2.add(registryURL, java.awt.BorderLayout.CENTER);
jPanel2.add(reset, java.awt.BorderLayout.EAST);
this.add(jPanel2, new GridBagConstraints(0, 2, 3, 1, 0.0, 0.0,
GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
new Insets(5, 10, 0, 10), 339, 0));
- this.add(jScrollPane2, new GridBagConstraints(0, 1, 1, 1, 1.0, 1.0,
- GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
- 0, 0, 0, 60), 80, 60));
- this.add(jScrollPane4, new GridBagConstraints(2, 1, 1, 1, 1.0, 1.0,
- GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
- 0, -80, 0, 0), 80, 60));
- this.add(jScrollPane3, new GridBagConstraints(1, 1, 1, 1, 1.0, 1.0,
- GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
- 0, -60, 0, 80), 80, 60));
+ this.add(jScrollPane2,
+ new GridBagConstraints(0, 1, 1, 1, 1.0, 1.0,
+ GridBagConstraints.CENTER, GridBagConstraints.BOTH,
+ new Insets(0, 0, 0, 60), 80, 60));
+ this.add(jScrollPane4,
+ new GridBagConstraints(2, 1, 1, 1, 1.0, 1.0,
+ GridBagConstraints.CENTER, GridBagConstraints.BOTH,
+ new Insets(0, -80, 0, 0), 80, 60));
+ this.add(jScrollPane3,
+ new GridBagConstraints(1, 1, 1, 1, 1.0, 1.0,
+ GridBagConstraints.CENTER, GridBagConstraints.BOTH,
+ new Insets(0, -60, 0, 80), 80, 60));
}
protected JTable table = new JTable();
VamsasMenu.setToolTipText(MessageManager
.getString("label.share_data_vamsas_applications"));
VamsasStMenu.setText(MessageManager.getString("label.connect_to"));
- VamsasStMenu.setToolTipText(MessageManager
- .getString("label.join_existing_vamsas_session"));
- inputLocalFileMenuItem.setText(MessageManager
- .getString("label.load_tree_from_file"));
- inputLocalFileMenuItem.setAccelerator(javax.swing.KeyStroke
- .getKeyStroke(java.awt.event.KeyEvent.VK_O, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false));
+ VamsasStMenu.setToolTipText(
+ MessageManager.getString("label.join_existing_vamsas_session"));
+ inputLocalFileMenuItem
+ .setText(MessageManager.getString("label.load_tree_from_file"));
+ inputLocalFileMenuItem.setAccelerator(
+ javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_O,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(),
+ false));
inputLocalFileMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
}
}
});
- inputTextboxMenuItem.setText(MessageManager
- .getString("label.from_textbox"));
+ inputTextboxMenuItem
+ .setText(MessageManager.getString("label.from_textbox"));
inputTextboxMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
aboutMenuItem_actionPerformed(e);
}
});
- documentationMenuItem.setText(MessageManager
- .getString("label.documentation"));
+ documentationMenuItem
+ .setText(MessageManager.getString("label.documentation"));
documentationMenuItem.setAccelerator(javax.swing.KeyStroke
.getKeyStroke(java.awt.event.KeyEvent.VK_F1, 0, false));
documentationMenuItem
}
});
inputMenu.setText(MessageManager.getString("label.input_alignment"));
- vamsasStart.setText(MessageManager
- .getString("label.new_vamsas_session"));
+ vamsasStart
+ .setText(MessageManager.getString("label.new_vamsas_session"));
vamsasStart.setVisible(false);
vamsasStart.addActionListener(new ActionListener()
{
vamsasStart_actionPerformed(e);
}
});
- vamsasImport.setText(MessageManager
- .getString("action.load_vamsas_session"));
+ vamsasImport.setText(
+ MessageManager.getString("action.load_vamsas_session"));
vamsasImport.setVisible(false);
vamsasImport.addActionListener(new ActionListener()
{
vamsasImport_actionPerformed(e);
}
});
- vamsasSave.setText(MessageManager
- .getString("action.save_vamsas_session"));
+ vamsasSave.setText(
+ MessageManager.getString("action.save_vamsas_session"));
vamsasSave.setVisible(false);
vamsasSave.addActionListener(new ActionListener()
{
vamsasSave_actionPerformed(e);
}
});
- inputSequence.setText(MessageManager
- .getString("action.fetch_sequences"));
+ inputSequence
+ .setText(MessageManager.getString("action.fetch_sequences"));
inputSequence.addActionListener(new ActionListener()
{
@Override
inputSequence_actionPerformed(e);
}
});
- vamsasStop.setText(MessageManager
- .getString("label.stop_vamsas_session"));
+ vamsasStop
+ .setText(MessageManager.getString("label.stop_vamsas_session"));
vamsasStop.setVisible(false);
vamsasStop.addActionListener(new ActionListener()
{
closeAll_actionPerformed(e);
}
});
- raiseRelated.setText(MessageManager
- .getString("action.raise_associated_windows"));
+ raiseRelated.setText(
+ MessageManager.getString("action.raise_associated_windows"));
raiseRelated.addActionListener(new ActionListener()
{
@Override
raiseRelated_actionPerformed(e);
}
});
- minimizeAssociated.setText(MessageManager
- .getString("action.minimize_associated_windows"));
+ minimizeAssociated.setText(
+ MessageManager.getString("action.minimize_associated_windows"));
minimizeAssociated.addActionListener(new ActionListener()
{
@Override
minimizeAssociated_actionPerformed(e);
}
});
- garbageCollect.setText(MessageManager
- .getString("label.collect_garbage"));
+ garbageCollect
+ .setText(MessageManager.getString("label.collect_garbage"));
garbageCollect.addActionListener(new ActionListener()
{
@Override
garbageCollect_actionPerformed(e);
}
});
- showMemusage.setText(MessageManager
- .getString("label.show_memory_usage"));
+ showMemusage
+ .setText(MessageManager.getString("label.show_memory_usage"));
showMemusage.addActionListener(new ActionListener()
{
@Override
}
});
experimentalFeatures = new JCheckBoxMenuItem();
- experimentalFeatures.setText(MessageManager
- .getString("label.show_experimental"));
- experimentalFeatures.setToolTipText(MessageManager
- .getString("label.show_experimental_tip"));
+ experimentalFeatures
+ .setText(MessageManager.getString("label.show_experimental"));
+ experimentalFeatures.setToolTipText(
+ MessageManager.getString("label.show_experimental_tip"));
experimentalFeatures.addActionListener(new ActionListener()
{
@Override
* @param e
* DOCUMENT ME!
*/
- protected void inputTextboxMenuItem_actionPerformed(AlignmentViewPanel avp)
+ protected void inputTextboxMenuItem_actionPerformed(
+ AlignmentViewPanel avp)
{
}
protected JButton createFeatures = new JButton();
- protected JvCacheableInputBox<String> searchBox = new JvCacheableInputBox<String>(getCacheKey());
+ protected JvCacheableInputBox<String> searchBox = new JvCacheableInputBox<String>(
+ getCacheKey());
BorderLayout mainBorderLayout = new BorderLayout();
searchBox.setFont(new java.awt.Font("Verdana", Font.PLAIN, 12));
((JTextComponent) searchBox.getEditor().getEditorComponent())
.addCaretListener(new CaretListener()
- {
- @Override
- public void caretUpdate(CaretEvent e)
- {
- textfield_caretUpdate(e);
- }
- });
+ {
+ @Override
+ public void caretUpdate(CaretEvent e)
+ {
+ textfield_caretUpdate(e);
+ }
+ });
searchBox.getEditor().getEditorComponent()
.addKeyListener(new java.awt.event.KeyAdapter()
{
caseSensitive.setHorizontalAlignment(SwingConstants.LEFT);
caseSensitive.setText(MessageManager.getString("label.match_case"));
- searchDescription.setText(MessageManager
- .getString("label.include_description"));
+ searchDescription
+ .setText(MessageManager.getString("label.include_description"));
actionsPanel.add(findNext, null);
actionsPanel.add(findAll, null);
{
}
-
public void createFeatures_actionPerformed()
{
}
if (al != null && al.getHeight() > 0)
{
str = jalview.analysis.AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars, al.getSequenceAt(0)
- .getSequenceAsString());
+ jalview.util.Comparison.GapChars,
+ al.getSequenceAt(0).getSequenceAsString());
}
}
}
}
-
-
-
-
/**
* Returns unique key used for storing Finder cache items in the cache data
* structure
return FINDER_CACHE_KEY;
}
-
-
}
}
});
JMenuItem outputProjPoints = new JMenuItem();
- outputProjPoints.setText(MessageManager
- .getString("label.output_transformed_points"));
+ outputProjPoints.setText(
+ MessageManager.getString("label.output_transformed_points"));
outputProjPoints.addActionListener(new ActionListener()
{
@Override
{
}
});
- scoreModelMenu.setText(MessageManager
- .getString("label.select_score_model"));
+ scoreModelMenu
+ .setText(MessageManager.getString("label.select_score_model"));
scoreModelMenu.addMenuListener(new MenuListener()
{
@Override
originalSeqData_actionPerformed(e);
}
});
- associateViewsMenu.setText(MessageManager
- .getString("label.associate_nodes_with"));
+ associateViewsMenu.setText(
+ MessageManager.getString("label.associate_nodes_with"));
calcSettings.setText(MessageManager.getString("action.change_params"));
nuclSetting
.setText(MessageManager.getString("label.nucleotide_matrix"));
textarea.setText("");
textarea.setWrapStyleWord(false);
viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12));
- viewInEditorButton.setText(MessageManager
- .getString("label.view_alignment_editor"));
- viewInEditorButton
- .addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- viewInEditorButton_actionPerformed(e);
- }
- });
+ viewInEditorButton.setText(
+ MessageManager.getString("label.view_alignment_editor"));
+ viewInEditorButton.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ viewInEditorButton_actionPerformed(e);
+ }
+ });
this.add(scrollPane, BorderLayout.CENTER);
scrollPane.getViewport().add(textarea, null);
this.add(jPanel1, BorderLayout.SOUTH);
{
private static final Font LABEL_FONT = JvSwingUtils.getLabelFont();
- private static final Font LABEL_FONT_ITALIC = JvSwingUtils.getLabelFont(
- false, true);
+ private static final Font LABEL_FONT_ITALIC = JvSwingUtils
+ .getLabelFont(false, true);
/*
* Visual tab components
JPanel editingTab = new JPanel();
editingTab.setLayout(null);
autoCalculateConsCheck.setFont(LABEL_FONT);
- autoCalculateConsCheck.setText(MessageManager
- .getString("label.autocalculate_consensus"));
+ autoCalculateConsCheck.setText(
+ MessageManager.getString("label.autocalculate_consensus"));
autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
padGaps.setFont(LABEL_FONT);
- padGaps.setText(MessageManager.getString("label.pad_gaps_when_editing"));
+ padGaps.setText(
+ MessageManager.getString("label.pad_gaps_when_editing"));
padGaps.setBounds(new Rectangle(22, 94, 168, 23));
sortByTree.setFont(LABEL_FONT);
sortByTree
.setText(MessageManager.getString("label.sort_with_new_tree"));
- sortByTree
- .setToolTipText(MessageManager
- .getString("label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
+ sortByTree.setToolTipText(MessageManager.getString(
+ "label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
editingTab.add(autoCalculateConsCheck);
editingTab.add(padGaps);
pirjv.setFont(LABEL_FONT);
pirjv.setHorizontalAlignment(SwingConstants.LEFT);
autoIdWidth.setFont(LABEL_FONT);
- autoIdWidth.setText(MessageManager
- .getString("label.automatically_set_id_width"));
- autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true,
- MessageManager
- .getString("label.adjusts_width_generated_eps_png")));
+ autoIdWidth.setText(
+ MessageManager.getString("label.automatically_set_id_width"));
+ autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
+ .getString("label.adjusts_width_generated_eps_png")));
autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
autoIdWidth.addActionListener(new ActionListener()
{
}
});
userIdWidthlabel.setFont(LABEL_FONT);
- userIdWidthlabel.setText(MessageManager
- .getString("label.figure_id_column_width"));
- userIdWidth
- .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
- .getString("label.manually_specify_width_left_column")));
- userIdWidthlabel
- .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
- .getString("label.manually_specify_width_left_column")));
+ userIdWidthlabel.setText(
+ MessageManager.getString("label.figure_id_column_width"));
+ userIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
+ .getString("label.manually_specify_width_left_column")));
+ userIdWidthlabel.setToolTipText(
+ JvSwingUtils.wrapTooltip(true, MessageManager.getString(
+ "label.manually_specify_width_left_column")));
userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
userIdWidth.setText("");
}
});
modellerOutput.setFont(LABEL_FONT);
- modellerOutput.setText(MessageManager
- .getString("label.use_modeller_output"));
+ modellerOutput
+ .setText(MessageManager.getString("label.use_modeller_output"));
modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
embbedBioJSON.setFont(LABEL_FONT);
embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson"));
JLabel browserLabel = new JLabel();
browserLabel.setFont(LABEL_FONT);
browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
- browserLabel.setText(MessageManager
- .getString("label.default_browser_unix"));
+ browserLabel.setText(
+ MessageManager.getString("label.default_browser_unix"));
defaultBrowser.setFont(LABEL_FONT);
defaultBrowser.setText("");
initConnTabCheckboxes();
// Add default Browser text box
- connectTab.add(browserLabel, new GridBagConstraints(0, 0, 1, 1, 0.0,
- 0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
- new Insets(10, 0, 5, 5), 5, 1));
+ connectTab.add(browserLabel,
+ new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.NONE,
+ new Insets(10, 0, 5, 5), 5, 1));
defaultBrowser.setFont(LABEL_FONT);
defaultBrowser.setText("");
new Insets(10, 0, 5, 12), 4, 10));
// Add usage stats, version check and questionnaire checkboxes
- connectTab.add(usagestats, new GridBagConstraints(0, 2, 1, 1, 1.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(0, 2, 5, 5), 70, 1));
- connectTab.add(questionnaire, new GridBagConstraints(1, 2, 1, 1, 1.0,
- 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(0, 2, 5, 10), 70, 1));
- connectTab.add(versioncheck, new GridBagConstraints(0, 3, 1, 1, 1.0,
- 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(0, 2, 5, 5), 70, 1));
+ connectTab.add(usagestats,
+ new GridBagConstraints(0, 2, 1, 1, 1.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 5, 5), 70, 1));
+ connectTab.add(questionnaire,
+ new GridBagConstraints(1, 2, 1, 1, 1.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 5, 10), 70, 1));
+ connectTab.add(versioncheck,
+ new GridBagConstraints(0, 3, 1, 1, 1.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 5, 5), 70, 1));
// Add padding so the panel doesn't look ridiculous
JPanel spacePanel = new JPanel();
- connectTab.add(spacePanel, new GridBagConstraints(0, 4, 1, 1, 1.0, 1.0,
- GridBagConstraints.WEST, GridBagConstraints.BOTH, new Insets(0,
- 0, 0, 5), 70, 1));
+ connectTab.add(spacePanel,
+ new GridBagConstraints(0, 4, 1, 1, 1.0, 1.0,
+ GridBagConstraints.WEST, GridBagConstraints.BOTH,
+ new Insets(0, 0, 0, 5), 70, 1));
return connectTab;
}
// Panel for links functionality
JPanel linkPanel = new JPanel(new GridBagLayout());
- linkPanel.setBorder(new TitledBorder(MessageManager
- .getString("label.url_linkfrom_sequence_id")));
+ linkPanel.setBorder(new TitledBorder(
+ MessageManager.getString("label.url_linkfrom_sequence_id")));
// Put the Url links panel together
// no current selection, so initially disable delete/edit buttons
editLink.setEnabled(false);
deleteLink.setEnabled(false);
-
+
newLink.addActionListener(new java.awt.event.ActionListener()
{
@Override
MessageManager.getString("label.proxy_server"));
proxyPanel.setBorder(titledBorder1);
proxyPanel.setLayout(new GridBagLayout());
- proxyPanel.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
- 0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
- new Insets(0, 2, 2, 0), 5, 0));
- proxyPanel.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
- 0, 2, 0), 11, 0));
- proxyPanel.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
- 2, 5, 185), 2, -4));
- proxyPanel.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0,
- 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(0, 2, 2, 2), 54, 1));
- proxyPanel.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0,
- 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(0, 2, 2, 0), 263, 1));
+ proxyPanel.add(serverLabel,
+ new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.NONE,
+ new Insets(0, 2, 2, 0), 5, 0));
+ proxyPanel.add(portLabel,
+ new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.NONE,
+ new Insets(0, 0, 2, 0), 11, 0));
+ proxyPanel.add(useProxy,
+ new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.NONE,
+ new Insets(0, 2, 5, 185), 2, -4));
+ proxyPanel.add(proxyPortTB,
+ new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 2, 2), 54, 1));
+ proxyPanel.add(proxyServerTB,
+ new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
+ GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
+ new Insets(0, 2, 2, 0), 263, 1));
return proxyPanel;
}
private void initConnTabCheckboxes()
{
// Usage stats checkbox label
- usagestats.setText(MessageManager
- .getString("label.send_usage_statistics"));
+ usagestats.setText(
+ MessageManager.getString("label.send_usage_statistics"));
usagestats.setFont(LABEL_FONT);
usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
// Questionnaire checkbox label
- questionnaire.setText(MessageManager
- .getString("label.check_for_questionnaires"));
+ questionnaire.setText(
+ MessageManager.getString("label.check_for_questionnaires"));
questionnaire.setFont(LABEL_FONT);
questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
// Check for latest version checkbox label
- versioncheck.setText(MessageManager
- .getString("label.check_for_latest_version"));
+ versioncheck.setText(
+ MessageManager.getString("label.check_for_latest_version"));
versioncheck.setFont(LABEL_FONT);
versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
private JPanel initColoursTab()
{
JPanel coloursTab = new JPanel();
- coloursTab.setBorder(new TitledBorder(MessageManager
- .getString("action.open_new_alignment")));
+ coloursTab.setBorder(new TitledBorder(
+ MessageManager.getString("action.open_new_alignment")));
coloursTab.setLayout(new FlowLayout());
JLabel mincolourLabel = new JLabel();
mincolourLabel.setFont(LABEL_FONT);
JLabel protColourLabel = new JLabel();
protColourLabel.setFont(LABEL_FONT);
protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
- protColourLabel.setText(MessageManager
- .getString("label.prot_alignment_colour") + " ");
- JvSwingUtils.addtoLayout(coloursTab, MessageManager
- .getString("label.default_colour_scheme_for_alignment"),
+ protColourLabel.setText(
+ MessageManager.getString("label.prot_alignment_colour") + " ");
+ JvSwingUtils.addtoLayout(coloursTab,
+ MessageManager
+ .getString("label.default_colour_scheme_for_alignment"),
protColourLabel, protColour);
nucColour.setFont(LABEL_FONT);
JLabel nucColourLabel = new JLabel();
nucColourLabel.setFont(LABEL_FONT);
nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
- nucColourLabel.setText(MessageManager
- .getString("label.nuc_alignment_colour") + " ");
- JvSwingUtils.addtoLayout(coloursTab, MessageManager
- .getString("label.default_colour_scheme_for_alignment"),
+ nucColourLabel.setText(
+ MessageManager.getString("label.nuc_alignment_colour") + " ");
+ JvSwingUtils.addtoLayout(coloursTab,
+ MessageManager
+ .getString("label.default_colour_scheme_for_alignment"),
nucColourLabel, nucColour);
JPanel annotationShding = new JPanel();
- annotationShding.setBorder(new TitledBorder(MessageManager
- .getString("label.annotation_shading_default")));
+ annotationShding.setBorder(new TitledBorder(
+ MessageManager.getString("label.annotation_shading_default")));
annotationShding.setLayout(new GridLayout(1, 2));
- JvSwingUtils.addtoLayout(annotationShding, MessageManager
- .getString("label.default_minimum_colour_annotation_shading"),
+ JvSwingUtils.addtoLayout(annotationShding,
+ MessageManager.getString(
+ "label.default_minimum_colour_annotation_shading"),
mincolourLabel, minColour);
- JvSwingUtils.addtoLayout(annotationShding, MessageManager
- .getString("label.default_maximum_colour_annotation_shading"),
+ JvSwingUtils.addtoLayout(annotationShding,
+ MessageManager.getString(
+ "label.default_maximum_colour_annotation_shading"),
maxcolourLabel, maxColour);
coloursTab.add(annotationShding); // , FlowLayout.LEFT);
return coloursTab;
{
structureTab = new JPanel();
- structureTab.setBorder(new TitledBorder(MessageManager
- .getString("label.structure_options")));
+ structureTab.setBorder(new TitledBorder(
+ MessageManager.getString("label.structure_options")));
structureTab.setLayout(null);
final int width = 400;
final int height = 22;
ypos += lineSpacing;
addSecondaryStructure.setFont(LABEL_FONT);
- addSecondaryStructure.setText(MessageManager
- .getString("label.autoadd_secstr"));
+ addSecondaryStructure
+ .setText(MessageManager.getString("label.autoadd_secstr"));
addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
structureTab.add(addSecondaryStructure);
@Override
public void actionPerformed(ActionEvent e)
{
- structureViewer_actionPerformed((String) structViewer
- .getSelectedItem());
+ structureViewer_actionPerformed(
+ (String) structViewer.getSelectedItem());
}
});
structureTab.add(structViewer);
JFileChooser chooser = new JFileChooser();
// chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager
- .getString("label.open_local_file"));
+ chooser.setDialogTitle(
+ MessageManager.getString("label.open_local_file"));
chooser.setToolTipText(MessageManager.getString("action.open"));
int value = chooser.showOpenDialog(this);
private JPanel initVisualTab()
{
JPanel visualTab = new JPanel();
- visualTab.setBorder(new TitledBorder(MessageManager
- .getString("action.open_new_alignment")));
+ visualTab.setBorder(new TitledBorder(
+ MessageManager.getString("action.open_new_alignment")));
visualTab.setLayout(null);
fullScreen.setFont(LABEL_FONT);
fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
showGroupbits.setFont(LABEL_FONT);
showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
- showGroupbits.setText(MessageManager.getString("action.show_group")
- + ":");
+ showGroupbits
+ .setText(MessageManager.getString("action.show_group") + ":");
JLabel showConsensbits = new JLabel();
showConsensbits.setFont(LABEL_FONT);
showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
- showConsensbits.setText(MessageManager.getString("label.consensus")
- + ":");
+ showConsensbits
+ .setText(MessageManager.getString("label.consensus") + ":");
showConsensHistogram.setEnabled(false);
showConsensHistogram.setFont(LABEL_FONT);
showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
showConsensHistogram.setSelected(true);
- showConsensHistogram.setText(MessageManager
- .getString("label.histogram"));
+ showConsensHistogram
+ .setText(MessageManager.getString("label.histogram"));
showConsensLogo.setEnabled(false);
showConsensLogo.setFont(LABEL_FONT);
showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
showGroupConservation.setSelected(true);
- showGroupConservation.setText(MessageManager
- .getString("label.conservation"));
+ showGroupConservation
+ .setText(MessageManager.getString("label.conservation"));
showNpTooltip.setEnabled(true);
showNpTooltip.setFont(LABEL_FONT);
showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
showNpTooltip.setSelected(true);
- showNpTooltip.setText(MessageManager
- .getString("label.non_positional_features"));
+ showNpTooltip.setText(
+ MessageManager.getString("label.non_positional_features"));
showDbRefTooltip.setEnabled(true);
showDbRefTooltip.setFont(LABEL_FONT);
showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
showDbRefTooltip.setSelected(true);
- showDbRefTooltip.setText(MessageManager
- .getString("label.database_references"));
+ showDbRefTooltip
+ .setText(MessageManager.getString("label.database_references"));
annotations.setFont(LABEL_FONT);
annotations.setHorizontalAlignment(SwingConstants.RIGHT);
annotations.setHorizontalTextPosition(SwingConstants.LEFT);
showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
showUnconserved.setSelected(true);
- showUnconserved.setText(MessageManager
- .getString("action.show_unconserved"));
+ showUnconserved
+ .setText(MessageManager.getString("action.show_unconserved"));
showUnconserved.addActionListener(new ActionListener()
{
@Override
scaleProteinToCdna.setFont(LABEL_FONT);
scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT);
scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING);
- scaleProteinToCdna.setText(MessageManager
- .getString("label.scale_protein_to_cdna"));
- scaleProteinToCdna.setToolTipText(MessageManager
- .getString("label.scale_protein_to_cdna_tip"));
+ scaleProteinToCdna.setText(
+ MessageManager.getString("label.scale_protein_to_cdna"));
+ scaleProteinToCdna.setToolTipText(
+ MessageManager.getString("label.scale_protein_to_cdna_tip"));
JLabel gapLabel = new JLabel();
gapLabel.setFont(LABEL_FONT);
gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
autoAnnotSettings.add(showConsensbits);
autoAnnotSettings.add(showConsensHistogram);
autoAnnotSettings.add(showConsensLogo);
-
-
JPanel tooltipSettings = new JPanel();
- tooltipSettings.setBorder(new TitledBorder(MessageManager
- .getString("label.sequence_id_tooltip")));
+ tooltipSettings.setBorder(new TitledBorder(
+ MessageManager.getString("label.sequence_id_tooltip")));
tooltipSettings.setBounds(173, 140, 220, 62);
tooltipSettings.setLayout(new GridLayout(2, 1));
tooltipSettings.add(showDbRefTooltip);
idItalics.setFont(LABEL_FONT_ITALIC);
idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
- idItalics.setText(MessageManager
- .getString("label.sequence_name_italics"));
+ idItalics.setText(
+ MessageManager.getString("label.sequence_name_italics"));
openoverv.setFont(LABEL_FONT);
- openoverv.setActionCommand(MessageManager
- .getString("label.open_overview"));
+ openoverv.setActionCommand(
+ MessageManager.getString("label.open_overview"));
openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
openoverv.setText(MessageManager.getString("label.open_overview"));
/**
* Customer renderer for JTable: supports column of radio buttons
*/
- public class RadioButtonRenderer extends JRadioButton implements
- TableCellRenderer
+ public class RadioButtonRenderer extends JRadioButton
+ implements TableCellRenderer
{
public RadioButtonRenderer()
{
// set colours to match rest of table
if (isSelected)
- {
- setBackground(table.getSelectionBackground());
- setForeground(table.getSelectionForeground());
- }
- else
- {
- setBackground(table.getBackground());
- setForeground(table.getForeground());
+ {
+ setBackground(table.getSelectionBackground());
+ setForeground(table.getSelectionForeground());
+ }
+ else
+ {
+ setBackground(table.getBackground());
+ setForeground(table.getForeground());
}
return this;
}
* Customer cell editor for JTable: supports column of radio buttons in
* conjunction with renderer
*/
- public class RadioButtonEditor extends AbstractCellEditor implements
- TableCellEditor
- {
- private JRadioButton button = new JRadioButton();
+ public class RadioButtonEditor extends AbstractCellEditor
+ implements TableCellEditor
+ {
+ private JRadioButton button = new JRadioButton();
- public RadioButtonEditor()
- {
+ public RadioButtonEditor()
+ {
button.setHorizontalAlignment(SwingConstants.CENTER);
this.button.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
{
- @Override
- public void actionPerformed(ActionEvent e)
- {
- fireEditingStopped();
- }
- });
- }
+ fireEditingStopped();
+ }
+ });
+ }
- @Override
- public Component getTableCellEditorComponent(JTable table,
- Object value, boolean isSelected, int row, int column)
- {
+ @Override
+ public Component getTableCellEditorComponent(JTable table, Object value,
+ boolean isSelected, int row, int column)
+ {
button.setSelected((boolean) value);
- return button;
- }
+ return button;
+ }
- @Override
- public Object getCellEditorValue()
- {
+ @Override
+ public Object getCellEditorValue()
+ {
return button.isSelected();
- }
+ }
}
}
protected void jbInit()
{
dpane = new JPanel(new MigLayout("", "[][][fill]", "[][fill][]"));
- dpane.setPreferredSize(new Dimension(
- 110 + 100 + OptsAndParamsPage.PARAM_WIDTH, 400));
+ dpane.setPreferredSize(
+ new Dimension(110 + 100 + OptsAndParamsPage.PARAM_WIDTH, 400));
typeList = new JList();
typeList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
- typeList.getSelectionModel().addListSelectionListener(
- new ListSelectionListener()
+ typeList.getSelectionModel()
+ .addListSelectionListener(new ListSelectionListener()
{
@Override
MessageManager.getString("label.input_parameter_name"),
new JLabel(MessageManager.getString("label.name")), tok,
"grow,spanx 3,wrap");
- JPanel paramsType = new JPanel(new MigLayout("", "[grow 100,fill]",
- "[grow 100,fill]"));
- paramsType.setBorder(new TitledBorder(MessageManager
- .getString("label.select_input_type")));
+ JPanel paramsType = new JPanel(
+ new MigLayout("", "[grow 100,fill]", "[grow 100,fill]"));
+ paramsType.setBorder(new TitledBorder(
+ MessageManager.getString("label.select_input_type")));
JScrollPane jlistScroller = new JScrollPane();
jlistScroller.setViewportView(typeList);
paramsType.add(jlistScroller, "spanx 2,spany 2");
dpane.add(paramsType);
- optionsPanel.setBorder(new TitledBorder(MessageManager
- .getString("label.set_options_for_type")));
+ optionsPanel.setBorder(new TitledBorder(
+ MessageManager.getString("label.set_options_for_type")));
optionsPanel.add(optionView);
dpane.add(optionsPanel, "wrap");
okcancel = new JPanel(new MigLayout("", "[center][center]", "[]"));
inputs.setLayout(new MigLayout("", "[grow 85,fill][]", ""));
paste = new JPanel();
paste.setName(MessageManager.getString("label.cut_paste"));
- paste.setLayout(new MigLayout("", "[grow 100, fill]",
- "[][grow 100,fill]"));
+ paste.setLayout(
+ new MigLayout("", "[grow 100, fill]", "[][grow 100,fill]"));
panels = new JTabbedPane();
panels.addTab(details.getName(), details);
cpanel = details;
name = new JTextArea(1, 12);
- JvSwingUtils.mgAddtoLayout(cpanel, MessageManager
- .getString("label.short_descriptive_name_for_service"),
+ JvSwingUtils.mgAddtoLayout(cpanel,
+ MessageManager
+ .getString("label.short_descriptive_name_for_service"),
new JLabel(MessageManager.getString("label.name")), name,
"wrap");
action = new JComboBox();
urlsuff = new JTextArea();
urlsuff.setColumns(60);
- JvSwingUtils.mgAddtoLayout(cpanel, MessageManager
- .getString("label.optional_suffix"),
+ JvSwingUtils.mgAddtoLayout(cpanel,
+ MessageManager.getString("label.optional_suffix"),
new JLabel(MessageManager.getString("label.url_suffix")),
urlsuff, "wrap");
});
vSeparable = new JCheckBox(
MessageManager.getString("label.result_vertically_separable"));
- vSeparable
- .setToolTipText(JvSwingUtils.wrapTooltip(
- true,
- MessageManager
- .getString("label.when_checked_job_visible_region_and_results")));
+ vSeparable.setToolTipText(
+ JvSwingUtils.wrapTooltip(true, MessageManager.getString(
+ "label.when_checked_job_visible_region_and_results")));
vSeparable.addActionListener(new ActionListener()
{
gapChar = new JComboBox();
JvSwingUtils.mgAddtoLayout(cpanel,
MessageManager.getString("label.preferred_gap_character"),
- new JLabel(MessageManager.getString("label.gap_character")
- + ":"), gapChar, "wrap");
+ new JLabel(
+ MessageManager.getString("label.gap_character") + ":"),
+ gapChar, "wrap");
cpanel.add(hSeparable);
cpanel.add(vSeparable);
// Input and Output lists
// Inputparams
JPanel iprmsList = new JPanel();
- iprmsList.setBorder(new TitledBorder(MessageManager
- .getString("label.data_input_parameters")));
+ iprmsList.setBorder(new TitledBorder(
+ MessageManager.getString("label.data_input_parameters")));
iprmsList.setLayout(new MigLayout("", "[grow 90, fill][]"));
iprmVp = new JScrollPane();
iprmVp.getViewport().setView(iprms = new JList());
});
JPanel rparamList = new JPanel();
- rparamList.setBorder(new TitledBorder(MessageManager
- .getString("label.data_returned_by_service")));
+ rparamList.setBorder(new TitledBorder(
+ MessageManager.getString("label.data_returned_by_service")));
rparamList.setLayout(new MigLayout("", "[grow 90, fill][]"));
rdata = new JList();
- rdata.setToolTipText(MessageManager
- .getString("label.right_click_to_edit_currently_selected_parameter"));
+ rdata.setToolTipText(MessageManager.getString(
+ "label.right_click_to_edit_currently_selected_parameter"));
rdata.addMouseListener(new MouseListener()
{
urldescVp = new JScrollPane();
urldescVp.setViewportView(urldesc);
JPanel urldescPane = new JPanel();
- urldescPane.setLayout(new MigLayout("", "[grow 100, fill]",
- "[grow 100, fill]"));
- urldescPane.setBorder(new TitledBorder(MessageManager
- .getString("label.rsbs_encoded_service")));
+ urldescPane.setLayout(
+ new MigLayout("", "[grow 100, fill]", "[grow 100, fill]"));
+ urldescPane.setBorder(new TitledBorder(
+ MessageManager.getString("label.rsbs_encoded_service")));
urldescPane.add(urldescVp, "span");
paste.add(urldescPane, "span");
urldescPane.setToolTipText(JvSwingUtils.wrapTooltip(true,
parseResVp.setViewportView(parseRes);
parseRes.setWrapStyleWord(true);
parseRes.setColumns(60);
- parseWarnings = new JPanel(new MigLayout("", "[grow 100, fill]",
- "[grow 100, fill]"));
- parseWarnings.setBorder(new TitledBorder(MessageManager
- .getString("label.parsing_errors")));
+ parseWarnings = new JPanel(
+ new MigLayout("", "[grow 100, fill]", "[grow 100, fill]"));
+ parseWarnings.setBorder(new TitledBorder(
+ MessageManager.getString("label.parsing_errors")));
parseWarnings.setToolTipText(JvSwingUtils.wrapTooltip(true,
MessageManager.getString("label.result_of_parsing_rsbs")));
parseWarnings.add(parseResVp, "center");
height = 176;
}
- this.add(jPanel1, new GridBagConstraints(0, 0, 1, 1, 1.0, 1.0,
- GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(
- 5, 4, 6, 5), 390, height));
+ this.add(jPanel1,
+ new GridBagConstraints(0, 0, 1, 1, 1.0, 1.0,
+ GridBagConstraints.CENTER, GridBagConstraints.BOTH,
+ new Insets(5, 4, 6, 5), 390, height));
}
@Override
allGroupsCheck.setEnabled(false);
allGroupsCheck.setFont(new java.awt.Font("Verdana", 0, 11));
allGroupsCheck.setOpaque(false);
- allGroupsCheck.setText(MessageManager
- .getString("action.apply_all_groups"));
+ allGroupsCheck
+ .setText(MessageManager.getString("action.apply_all_groups"));
allGroupsCheck.addActionListener(new java.awt.event.ActionListener()
{
@Override
return false;
}
Point p = comp.getLocationOnScreen();
- Rectangle r = new Rectangle(p.x, p.y, comp.getWidth(), comp.getHeight());
+ Rectangle r = new Rectangle(p.x, p.y, comp.getWidth(),
+ comp.getHeight());
return r.contains(loc);
}
else
{
this.dividerRatio = splitPane.getDividerLocation()
- / (double) (splitPane.getHeight() - splitPane
- .getDividerSize());
+ / (double) (splitPane.getHeight()
+ - splitPane.getDividerSize());
}
if (alignFrame == this.topFrame)
@SuppressWarnings("serial")
/**
- * GUI layout for structure chooser
+ * GUI layout for structure chooser
+ *
* @author tcnofoegbu
*
*/
-public abstract class GStructureChooser extends JPanel implements
- ItemListener
+public abstract class GStructureChooser extends JPanel
+ implements ItemListener
{
protected JPanel statusPanel = new JPanel();
protected JCheckBox chk_invertFilter = new JCheckBox(
MessageManager.getString("label.invert"));
- protected ImageIcon loadingImage = new ImageIcon(getClass().getResource(
- "/images/loading.gif"));
+ protected ImageIcon loadingImage = new ImageIcon(
+ getClass().getResource("/images/loading.gif"));
- protected ImageIcon goodImage = new ImageIcon(getClass().getResource(
- "/images/good.png"));
+ protected ImageIcon goodImage = new ImageIcon(
+ getClass().getResource("/images/good.png"));
- protected ImageIcon errorImage = new ImageIcon(getClass().getResource(
- "/images/error.png"));
+ protected ImageIcon errorImage = new ImageIcon(
+ getClass().getResource("/images/error.png"));
- protected ImageIcon warningImage = new ImageIcon(getClass().getResource(
- "/images/warning.gif"));
+ protected ImageIcon warningImage = new ImageIcon(
+ getClass().getResource("/images/warning.gif"));
protected JLabel lbl_warning = new JLabel(warningImage);
// e.printStackTrace();
}
toolTipText = (toolTipText == null ? null
- : (toolTipText.length() > 500 ? JvSwingUtils.wrapTooltip(
- true, "\"" + toolTipText.subSequence(0, 500)
- + "...\"") : JvSwingUtils.wrapTooltip(true,
- toolTipText)));
+ : (toolTipText.length() > 500
+ ? JvSwingUtils.wrapTooltip(true,
+ "\"" + toolTipText.subSequence(0, 500)
+ + "...\"")
+ : JvSwingUtils.wrapTooltip(true, toolTipText)));
return toolTipText;
}
};
*/
private void jbInit() throws Exception
{
- Integer width = tempUserPrefs.get("structureChooser.width") == null ? 800
+ Integer width = tempUserPrefs.get("structureChooser.width") == null
+ ? 800
: tempUserPrefs.get("structureChooser.width");
- Integer height = tempUserPrefs.get("structureChooser.height") == null ? 400
+ Integer height = tempUserPrefs.get("structureChooser.height") == null
+ ? 400
: tempUserPrefs.get("structureChooser.height");
tbl_summary.setAutoCreateRowSorter(true);
tbl_summary.getTableHeader().setReorderingAllowed(false);
scrl_foundStructures.setPreferredSize(new Dimension(width, height));
scrl_localPDB.setPreferredSize(new Dimension(width, height));
- scrl_localPDB
- .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
+ scrl_localPDB.setHorizontalScrollBarPolicy(
+ JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
cmb_filterOption.setFont(new java.awt.Font("Verdana", 0, 12));
chk_invertFilter.setFont(new java.awt.Font("Verdana", 0, 12));
chk_rememberSettings.setVisible(false);
txt_search.setToolTipText(JvSwingUtils.wrapTooltip(true,
MessageManager.getString("label.enter_pdb_id")));
- cmb_filterOption.setToolTipText(MessageManager
- .getString("info.select_filter_option"));
+ cmb_filterOption.setToolTipText(
+ MessageManager.getString("info.select_filter_option"));
txt_search.getDocument().addDocumentListener(new DocumentListener()
{
@Override
btn_view.setVisible(false);
btn_cancel.setVisible(false);
previousWantedFields = pdbDocFieldPrefs
- .getStructureSummaryFields().toArray(
- new FTSDataColumnI[0]);
+ .getStructureSummaryFields()
+ .toArray(new FTSDataColumnI[0]);
}
if (sourceTabbedPane.getTitleAt(index)
.equals(foundStructureSummary))
statusPanel.add(statusBar, null);
this.add(pnl_actionsAndStatus, java.awt.BorderLayout.SOUTH);
- mainFrame
- .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+ mainFrame.addInternalFrameListener(
+ new javax.swing.event.InternalFrameAdapter()
{
@Override
public void internalFrameClosing(InternalFrameEvent e)
public AssociateSeqOptions(SequenceI seq)
{
this.sequence = seq;
- this.name = (seq.getName().length() >= 23) ? seq.getName().substring(
- 0, 23) : seq.getName();
+ this.name = (seq.getName().length() >= 23)
+ ? seq.getName().substring(0, 23)
+ : seq.getName();
}
public AssociateSeqOptions(String name, SequenceI seq)
this.setLayout(new FlowLayout());
this.add(cmb_assSeq);
this.add(lbl_associateSeq);
- cmb_assSeq.setToolTipText(MessageManager
- .getString("info.associate_wit_sequence"));
+ cmb_assSeq.setToolTipText(
+ MessageManager.getString("info.associate_wit_sequence"));
cmb_assSeq.addItemListener(this);
}
* @author tcnofoegbu
*
*/
- public abstract class CustomComboSeparatorsRenderer implements
- ListCellRenderer<Object>
+ public abstract class CustomComboSeparatorsRenderer
+ implements ListCellRenderer<Object>
{
private ListCellRenderer<Object> regent;
private JSeparator jSeparator = new JSeparator();
- public CustomComboSeparatorsRenderer(ListCellRenderer<Object> listCellRenderer)
+ public CustomComboSeparatorsRenderer(
+ ListCellRenderer<Object> listCellRenderer)
{
this.regent = listCellRenderer;
}
@Override
- public Component getListCellRendererComponent(JList list,
- Object value,
+ public Component getListCellRendererComponent(JList list, Object value,
int index, boolean isSelected, boolean cellHasFocus)
{
index, isSelected, cellHasFocus);
if (index != -1
&& addSeparatorAfter(list, (FilterOption) value, index))
- {
+ {
separatorPanel.removeAll();
separatorPanel.add(comp, BorderLayout.CENTER);
separatorPanel.add(jSeparator, BorderLayout.SOUTH);
}
protected abstract boolean addSeparatorAfter(JList list,
- FilterOption value,
- int index);
+ FilterOption value, int index);
}
protected abstract void stateChanged(ItemEvent e);
protected abstract void txt_search_ActionPerformed();
public abstract void populateCmbAssociateSeqOptions(
- JComboBox<AssociateSeqOptions> cmb_assSeq, JLabel lbl_associateSeq);
+ JComboBox<AssociateSeqOptions> cmb_assSeq,
+ JLabel lbl_associateSeq);
public abstract void cmbAssSeqStateChanged();
import javax.swing.JPanel;
import javax.swing.JRadioButtonMenuItem;
-public abstract class GStructureViewer extends JInternalFrame implements
- JalviewStructureDisplayI, ColourChangeListener
+public abstract class GStructureViewer extends JInternalFrame
+ implements JalviewStructureDisplayI, ColourChangeListener
{
// private AAStructureBindingModel bindingModel;
fileMenu.setText(MessageManager.getString("action.file"));
savemenu = new JMenu();
- savemenu.setActionCommand(MessageManager.getString("action.save_image"));
+ savemenu.setActionCommand(
+ MessageManager.getString("action.save_image"));
savemenu.setText(MessageManager.getString("action.save_as"));
JMenuItem pdbFile = new JMenuItem();
}
});
alignStructs = new JMenuItem();
- alignStructs.setText(MessageManager
- .getString("label.superpose_structures"));
+ alignStructs.setText(
+ MessageManager.getString("label.superpose_structures"));
alignStructs.addActionListener(new ActionListener()
{
@Override
{
}
});
- sortAssocViews.setText(MessageManager
- .getString("label.sort_alignment_by_tree"));
+ sortAssocViews.setText(
+ MessageManager.getString("label.sort_alignment_by_tree"));
sortAssocViews.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
font_actionPerformed(e);
}
});
- bootstrapMenu.setText(MessageManager
- .getString("label.show_bootstrap_values"));
+ bootstrapMenu.setText(
+ MessageManager.getString("label.show_bootstrap_values"));
bootstrapMenu.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
saveAsMenu.setText(MessageManager.getString("action.save_as"));
- placeholdersMenu
- .setToolTipText(MessageManager
- .getString("label.marks_leaves_tree_not_associated_with_sequence"));
- placeholdersMenu.setText(MessageManager
- .getString("label.mark_unlinked_leaves"));
+ placeholdersMenu.setToolTipText(MessageManager.getString(
+ "label.marks_leaves_tree_not_associated_with_sequence"));
+ placeholdersMenu.setText(
+ MessageManager.getString("label.mark_unlinked_leaves"));
placeholdersMenu.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
originalSeqData_actionPerformed(e);
}
});
- associateLeavesMenu.setText(MessageManager
- .getString("label.associate_leaves_with"));
+ associateLeavesMenu.setText(
+ MessageManager.getString("label.associate_leaves_with"));
this.getContentPane().add(scrollPane, BorderLayout.CENTER);
jMenuBar1.add(fileMenu);
jMenuBar1.add(viewMenu);
label.setFont(new java.awt.Font("Verdana", Font.ITALIC, 10));
label.setOpaque(false);
label.setPreferredSize(new Dimension(260, 34));
- label.setText(MessageManager
- .formatMessage(
- "label.html_content",
- new String[] { MessageManager
- .getString("label.save_colour_scheme_with_unique_name_added_to_colour_menu") }));
+ label.setText(
+ MessageManager.formatMessage("label.html_content", new String[]
+ { MessageManager.getString(
+ "label.save_colour_scheme_with_unique_name_added_to_colour_menu") }));
caseSensitive.setText(MessageManager.getString("label.case_sensitive"));
caseSensitive.addActionListener(new ActionListener()
{
});
lcaseColour
.setText(MessageManager.getString("label.lower_case_colour"));
- lcaseColour.setToolTipText(MessageManager
- .getString("label.lower_case_tip"));
+ lcaseColour.setToolTipText(
+ MessageManager.getString("label.lower_case_tip"));
saveLoadPanel.add(savebutton);
saveLoadPanel.add(loadbutton);
// Java 7 default has 5 options rather than 3 for choosing colours; keep
// the first only
colorChooser
- .setChooserPanels(new AbstractColorChooserPanel[] { choosers[0] });
+ .setChooserPanels(new AbstractColorChooserPanel[]
+ { choosers[0] });
}
selectedButtons = new ArrayList<JButton>();
});
buttonPanel.setLayout(gridBagLayout1);
buttonPanel.setOpaque(false);
- showResultsNewFrame.setText(MessageManager
- .getString("label.new_window"));
+ showResultsNewFrame
+ .setText(MessageManager.getString("label.new_window"));
mergeResults.setText(MessageManager.getString("action.merge_results"));
this.setBackground(Color.white);
this.add(jPanel1, BorderLayout.NORTH);
jScrollPane1.getViewport().add(infoText, null);
jPanel1.add(titlePanel, BorderLayout.NORTH);
titlePanel.add(buttonPanel, BorderLayout.EAST);
- buttonPanel.add(cancel, new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0,
- GridBagConstraints.CENTER, GridBagConstraints.NONE, new Insets(
- 19, 6, 16, 4), 0, 0));
+ buttonPanel.add(cancel,
+ new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0,
+ GridBagConstraints.CENTER, GridBagConstraints.NONE,
+ new Insets(19, 6, 16, 4), 0, 0));
this.add(statusPanel, java.awt.BorderLayout.SOUTH);
statusPanel.add(statusBar, null);
}
});
enableJws2Services
.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- enableJws2Services.setText(MessageManager
- .getString("label.enable_jabaws_services"));
+ enableJws2Services.setText(
+ MessageManager.getString("label.enable_jabaws_services"));
enableJws2Services.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
displayWsWarning.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- displayWsWarning.setText(MessageManager
- .getString("label.display_warnings"));
displayWsWarning
- .setToolTipText("<html>"
- + MessageManager
- .getString("label.option_want_informed_web_service_URL_cannot_be_accessed_jalview_when_starts_up"));
+ .setText(MessageManager.getString("label.display_warnings"));
+ displayWsWarning.setToolTipText("<html>" + MessageManager.getString(
+ "label.option_want_informed_web_service_URL_cannot_be_accessed_jalview_when_starts_up"));
displayWsWarning.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
});
deleteWsUrl.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- deleteWsUrl.setText(MessageManager
- .getString("label.delete_service_url"));
+ deleteWsUrl
+ .setText(MessageManager.getString("label.delete_service_url"));
deleteWsUrl.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
});
moveWsUrlUp.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
moveWsUrlUp.setText(MessageManager.getString("action.move_up"));
- moveWsUrlUp.setToolTipText(MessageManager
- .getString("label.move_url_up"));
+ moveWsUrlUp
+ .setToolTipText(MessageManager.getString("label.move_url_up"));
moveWsUrlUp.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
});
moveWsUrlDown.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
moveWsUrlDown.setText(MessageManager.getString("action.move_down"));
- moveWsUrlDown.setToolTipText(MessageManager
- .getString("label.move_url_down"));
+ moveWsUrlDown.setToolTipText(
+ MessageManager.getString("label.move_url_down"));
moveWsUrlDown.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
newSbrsUrl.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- newSbrsUrl.setText(MessageManager
- .getString("label.add_sbrs_definition"));
+ newSbrsUrl
+ .setText(MessageManager.getString("label.add_sbrs_definition"));
newSbrsUrl.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
editSbrsUrl.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- editSbrsUrl.setText(MessageManager
- .getString("label.edit_sbrs_definition"));
+ editSbrsUrl.setText(
+ MessageManager.getString("label.edit_sbrs_definition"));
editSbrsUrl.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
});
deleteSbrsUrl.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- deleteSbrsUrl.setText(MessageManager
- .getString("label.delete_sbrs_definition"));
+ deleteSbrsUrl.setText(
+ MessageManager.getString("label.delete_sbrs_definition"));
deleteSbrsUrl.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
.get("latestReleaseVersion");
JSONArray repositoriesJsonArray = (JSONArray) JsonObj.get("releases");
- for (Iterator<JSONObject> repoIter = repositoriesJsonArray.iterator(); repoIter
- .hasNext();)
+ for (Iterator<JSONObject> repoIter = repositoriesJsonArray
+ .iterator(); repoIter.hasNext();)
{
JSONObject repoObj = repoIter.next();
BioJSReleasePojo repo = new BioJSReleasePojo();
@Attributes(
required = false,
- enums = { "0", "1", "2" },
+ enums =
+ { "0", "1", "2" },
description = "Determines the rendering for the annotation<br><ul><li>0 - No graph</li><li>1 - Bar Graph</li><li>2 - Line graph</li></ul>")
private int graphType;
@Attributes(
required = false,
- enums = { "None", "User Defined", "Clustal", "Zappo", "Taylor",
- "Nucleotide", "Pyrimidine", "Purine", "Turn", "Helix", "Strand",
- "Buried", "Hydro", "T-Coffee Scores", "RNA Interaction type",
- "Blosum62", "RNA Helices", "% Identity" },
+ enums =
+ { "None", "User Defined", "Clustal", "Zappo", "Taylor", "Nucleotide",
+ "Pyrimidine", "Purine", "Turn", "Helix", "Strand", "Buried",
+ "Hydro", "T-Coffee Scores", "RNA Interaction type", "Blosum62",
+ "RNA Helices", "% Identity" },
description = "The <a href=\"#colourScheme\">Colour Scheme</a> applied to the alignment")
private String colourScheme;
@Attributes(
required = true,
- enums = { "E", "H", "\u0000", ")", "(" },
+ enums =
+ { "E", "H", "\u0000", ")", "(" },
description = "Determines what is rendered for the secondary </br>structure <ul><li>’E’ - indicates Beta Sheet/Strand <li>’H’ - indicates alpha helix </li><li> ‘\\u0000’ - indicates blank</li></ul></br>For RNA Helix (only shown when working with</br> nucleotide sequences): <ul><li> ‘(’ - indicates bases pair with columns upstream</br> (to right) </li><li> ’(’ - indicate region pairs with bases to the left</li></ul>")
private char secondaryStructure;
@Attributes(required = true, description = "Sequence name")
private String name;
- @Attributes(required = false, description = "Sequence type", enums = {
- "DNA", "RNA", "Protein" })
+ @Attributes(
+ required = false,
+ description = "Sequence type",
+ enums =
+ { "DNA", "RNA", "Protein" })
private String type;
@Attributes(
{
}
- public SequencePojo(int start, int end, String id, String name, String seq)
+ public SequencePojo(int start, int end, String id, String name,
+ String seq)
{
this.id = id;
this.name = name;
{
}
-
+
/**
* Creates a new Matrix object containing a copy of the supplied array values.
* For example
if (iter == maxIter)
{
throw new Exception(MessageManager.formatMessage(
- "exception.matrix_too_many_iteration", new String[] {
- "tqli", Integer.valueOf(maxIter).toString() }));
+ "exception.matrix_too_many_iteration", new String[]
+ { "tqli", Integer.valueOf(maxIter).toString() }));
}
else
{
{
f = getValue(k - 1, i);
setValue(k - 1, i, (s * getValue(k - 1, i - 1)) + (c * f));
- setValue(k - 1, i - 1, (c * getValue(k - 1, i - 1)) - (s * f));
+ setValue(k - 1, i - 1,
+ (c * getValue(k - 1, i - 1)) - (s * f));
}
}
if (iter == maxIter)
{
throw new Exception(MessageManager.formatMessage(
- "exception.matrix_too_many_iteration", new String[] {
- "tqli2", Integer.valueOf(maxIter).toString() }));
+ "exception.matrix_too_many_iteration", new String[]
+ { "tqli2", Integer.valueOf(maxIter).toString() }));
}
else
{
*
* @param ps
* DOCUMENT ME!
- * @param format TODO
+ * @param format
+ * TODO
*/
@Override
public void printE(PrintStream ps, String format)
{
return e;
}
-
+
@Override
- public int height() {
+ public int height()
+ {
return rows;
}
* @return
*/
double[] getRow(int i);
-
+
MatrixI copy();
MatrixI transpose();
*/
public void print()
{
- System.out.println(matrix[0][0] + " " + matrix[0][1] + " "
- + matrix[0][2]);
+ System.out.println(
+ matrix[0][0] + " " + matrix[0][1] + " " + matrix[0][2]);
- System.out.println(matrix[1][0] + " " + matrix[1][1] + " "
- + matrix[1][2]);
+ System.out.println(
+ matrix[1][0] + " " + matrix[1][1] + " " + matrix[1][2]);
- System.out.println(matrix[2][0] + " " + matrix[2][1] + " "
- + matrix[2][2]);
+ System.out.println(
+ matrix[2][0] + " " + matrix[2][1] + " " + matrix[2][2]);
}
/**
public SparseMatrix(double[][] v)
{
rows = v.length;
- if (rows > 0) {
+ if (rows > 0)
+ {
cols = v[0].length;
}
sparseColumns = new SparseDoubleArray[cols];
ResidueShaderI profcolour = null;
private ColumnSelection columnSelection;
-
+
private HiddenColumns hiddenColumns;
private ProfilesI hconsensus;
* display a backward arrow
*/
g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
- new int[] { y + iconOffset, y + 14 + iconOffset,
- y + 8 + iconOffset }, 3);
+ new int[]
+ { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
+ 3);
x1 += 5;
}
if (diffdownstream)
* if annotation ending with an opeing base pair half of the stem,
* display a forward arrow
*/
- g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 }, new int[] {
- y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
+ g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 },
+ new int[]
+ { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
+ 3);
x2 -= 5;
}
if (diffupstream)
boolean diffdownstream = !validRes || !validEnd
|| row_annotations[column] == null
|| !dc.equals(row_annotations[column].displayCharacter);
- // System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream);
+ // System.out.println("Column "+column+" diff up: "+diffupstream+"
+ // down:"+diffdownstream);
// If a closing base pair half of the stem, display a backward arrow
if (column > 0 && Rna.isClosingParenthesis(dc))
{
// dc.equals(row_annotations[column-2].displayCharacter))
{
g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
- new int[] { y + iconOffset, y + 14 + iconOffset,
- y + 8 + iconOffset }, 3);
+ new int[]
+ { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
+ 3);
x1 += 5;
}
if (diffdownstream)
// display a forward arrow
if (diffdownstream)
{
- g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 }, new int[] {
- y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
+ g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 },
+ new int[]
+ { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
+ 3);
x2 -= 5;
}
if (diffupstream)
* the alignment has no colourscheme set
* (would like to use user preference but n/a for applet)
*/
- ColourSchemeI col = av.getAlignment().isNucleotide() ? new NucleotideColourScheme()
+ ColourSchemeI col = av.getAlignment().isNucleotide()
+ ? new NucleotideColourScheme()
: new ZappoColourScheme();
profcolour = new ResidueShader(col);
}
// properties/rendering attributes as a global 'alignment group' which holds
// all vis settings for the alignment as a whole rather than a subset
//
- if (aa.autoCalculated
- && (aa.label.startsWith("Consensus") || aa.label
- .startsWith("cDNA Consensus")))
+ if (aa.autoCalculated && (aa.label.startsWith("Consensus")
+ || aa.label.startsWith("cDNA Consensus")))
{
boolean forComplement = aa.label.startsWith("cDNA Consensus");
if (aa.groupRef != null && aa.groupRef.consensusData != null
{
if (forComplement)
{
- return AAFrequency.extractCdnaProfile(
- complementConsensus[column], av_ignoreGapsConsensus);
+ return AAFrequency.extractCdnaProfile(complementConsensus[column],
+ av_ignoreGapsConsensus);
}
else
{
- return AAFrequency.extractProfile(
-hconsensus.get(column),
+ return AAFrequency.extractProfile(hconsensus.get(column),
av_ignoreGapsConsensus);
}
}
.getAlignmentStrucConsensusAnnotation();
final AlignmentAnnotation complementConsensusAnnot = av
.getComplementConsensusAnnotation();
- boolean renderHistogram = true, renderProfile = true, normaliseProfile = false, isRNA = rna;
+ boolean renderHistogram = true, renderProfile = true,
+ normaliseProfile = false, isRNA = rna;
BitSet graphGroupDrawn = new BitSet();
int charOffset = 0; // offset for a label
lastSS = ' ';
lastSSX = 0;
- if (!useClip
- || ((y - charHeight) < visHeight && (y + row.height + charHeight * 2) >= sOffset))
+ if (!useClip || ((y - charHeight) < visHeight
+ && (y + row.height + charHeight * 2) >= sOffset))
{// if_in_visible_region
if (!clipst)
{
{
y += charHeight;
usedFaded = true;
- g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y
- - row.height, imgWidth, y, annotationPanel);
+ g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0,
+ y - row.height, imgWidth, y, annotationPanel);
g.setColor(Color.black);
// g.drawString("Calculating "+aa[i].label+"....",20, y-row.height/2);
{
validRes = true;
}
- final String displayChar = validRes ? row_annotations[column].displayCharacter
+ final String displayChar = validRes
+ ? row_annotations[column].displayCharacter
: null;
if (x > -1)
{
if (column == 0 || row.graph > 0)
{
- g.drawString(displayChar, (x * charWidth) + charOffset, y
- + iconOffset);
+ g.drawString(displayChar, (x * charWidth) + charOffset,
+ y + iconOffset);
}
- else if (row_annotations[column - 1] == null
- || (labelAllCols
- || !displayChar
- .equals(row_annotations[column - 1].displayCharacter) || (displayChar
- .length() < 2 && row_annotations[column].secondaryStructure == ' ')))
+ else if (row_annotations[column - 1] == null || (labelAllCols
+ || !displayChar.equals(
+ row_annotations[column - 1].displayCharacter)
+ || (displayChar.length() < 2
+ && row_annotations[column].secondaryStructure == ' ')))
{
- g.drawString(displayChar, x * charWidth + charOffset, y
- + iconOffset);
+ g.drawString(displayChar, x * charWidth + charOffset,
+ y + iconOffset);
}
g.setFont(ofont);
}
{
int nb_annot = x - temp;
- // System.out.println("\t type :"+lastSS+"\t x :"+x+"\t nbre annot :"+nb_annot);
+ // System.out.println("\t type :"+lastSS+"\t x :"+x+"\t nbre
+ // annot :"+nb_annot);
switch (lastSS)
{
case '(': // Stem case for RNA secondary structure
break;
default:
g.setColor(Color.gray);
- g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth)
- - lastSSX, 2);
+ g.fillRect(lastSSX, y + 6 + iconOffset,
+ (x * charWidth) - lastSSX, 2);
temp = x;
break;
}
{
clipend = true;
}
- }// end if_in_visible_region
+ } // end if_in_visible_region
if (row.graph > 0 && row.hasText)
{
y += charHeight;
{
if (clipst)
{
- System.err.println("Start clip at : " + yfrom + " (index " + f_i
- + ")");
+ System.err.println(
+ "Start clip at : " + yfrom + " (index " + f_i + ")");
}
if (clipend)
{
- System.err.println("End clip at : " + yto + " (index " + f_to
- + ")");
+ System.err.println(
+ "End clip at : " + yto + " (index " + f_to + ")");
}
}
;
private Color sdNOTCANONICAL_COLOUR;
void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX, int x,
- int y, int iconOffset, int startRes, int column,
- boolean validRes, boolean validEnd)
+ int y, int iconOffset, int startRes, int column, boolean validRes,
+ boolean validEnd)
{
g.setColor(GLYPHLINE_COLOR);
g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2);
void drawSheetAnnot(Graphics g, Annotation[] row,
- int lastSSX, int x, int y, int iconOffset, int startRes, int column,
- boolean validRes, boolean validEnd)
+ int lastSSX, int x, int y, int iconOffset, int startRes,
+ int column, boolean validRes, boolean validEnd)
{
g.setColor(SHEET_COLOUR);
if (!validEnd || !validRes || row == null || row[column] == null
|| row[column].secondaryStructure != 'E')
{
- g.fillRect(lastSSX, y + 4 + iconOffset,
- (x * charWidth) - lastSSX - 4, 7);
- g.fillPolygon(new int[] { (x * charWidth) - 4, (x * charWidth) - 4,
- (x * charWidth) }, new int[] { y + iconOffset,
- y + 14 + iconOffset, y + 7 + iconOffset }, 3);
+ g.fillRect(lastSSX, y + 4 + iconOffset, (x * charWidth) - lastSSX - 4,
+ 7);
+ g.fillPolygon(
+ new int[]
+ { (x * charWidth) - 4, (x * charWidth) - 4, (x * charWidth) },
+ new int[]
+ { y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset },
+ 3);
}
else
{
- g.fillRect(lastSSX, y + 4 + iconOffset,
- (x + 1) * charWidth - lastSSX, 7);
+ g.fillRect(lastSSX, y + 4 + iconOffset, (x + 1) * charWidth - lastSSX,
+ 7);
}
}
void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX, int x,
- int y, int iconOffset, int startRes, int column,
- boolean validRes, boolean validEnd)
+ int y, int iconOffset, int startRes, int column, boolean validRes,
+ boolean validEnd)
{
g.setColor(HELIX_COLOUR);
else
{
// g.setColor(Color.magenta);
- g.fillRoundRect(lastSSX + ofs, y + 4 + iconOffset, x2 - x1 - ofs
- + 1, 8, 0, 0);
+ g.fillRoundRect(lastSSX + ofs, y + 4 + iconOffset,
+ x2 - x1 - ofs + 1, 8, 0, 0);
}
}
void drawLineGraph(Graphics g, AlignmentAnnotation _aa,
- Annotation[] aa_annotations, int sRes, int eRes, int y,
- float min, float max, int graphHeight)
+ Annotation[] aa_annotations, int sRes, int eRes, int y, float min,
+ float max, int graphHeight)
{
if (sRes > aa_annotations.length)
{
g.setColor(aa_annotations[column].colour);
}
- y1 = y
- - (int) (((aa_annotations[column - 1].value - min) / range) * graphHeight);
- y2 = y
- - (int) (((aa_annotations[column].value - min) / range) * graphHeight);
+ y1 = y - (int) (((aa_annotations[column - 1].value - min) / range)
+ * graphHeight);
+ y2 = y - (int) (((aa_annotations[column].value - min) / range)
+ * graphHeight);
- g.drawLine(x * charWidth - charWidth / 2, y1, x * charWidth
- + charWidth / 2, y2);
+ g.drawLine(x * charWidth - charWidth / 2, y1,
+ x * charWidth + charWidth / 2, y2);
x++;
}
g.setColor(_aa.threshold.colour);
Graphics2D g2 = (Graphics2D) g;
g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
- BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f }, 0f));
+ BasicStroke.JOIN_ROUND, 3f, new float[]
+ { 5f, 3f }, 0f));
y2 = (int) (y - ((_aa.threshold.value - min) / range) * graphHeight);
g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
g.setColor(aa_annotations[column].colour);
}
- y1 = y
- - (int) (((aa_annotations[column].value - min) / (range)) * _aa.graphHeight);
+ y1 = y - (int) (((aa_annotations[column].value - min) / (range))
+ * _aa.graphHeight);
if (renderHistogram)
{
ht += scl;
// next profl[] position is profile % for the character(s)
scl = htn * scale * profl[c++];
- lm = ofont.getLineMetrics(dc, 0, 1, g.getFontMetrics()
- .getFontRenderContext());
- Font font = ofont.deriveFont(AffineTransform.getScaleInstance(
- wdth, scl / lm.getAscent()));
+ lm = ofont.getLineMetrics(dc, 0, 1,
+ g.getFontMetrics().getFontRenderContext());
+ Font font = ofont.deriveFont(AffineTransform
+ .getScaleInstance(wdth, scl / lm.getAscent()));
g.setFont(font);
lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g);
}
g.setColor(colour == Color.white ? Color.lightGray : colour);
- hght = (ht + (scl - lm.getDescent() - lm.getBaselineOffsets()[lm
- .getBaselineIndex()]));
+ hght = (ht + (scl - lm.getDescent()
+ - lm.getBaselineOffsets()[lm.getBaselineIndex()]));
g.drawChars(dc, 0, dc.length, x * charWidth, (int) hght);
valuesProcessed++;
g.setColor(_aa.threshold.colour);
Graphics2D g2 = (Graphics2D) g;
g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
- BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f }, 0f));
+ BasicStroke.JOIN_ROUND, 3f, new float[]
+ { 5f, 3f }, 0f));
- y2 = (int) (y - ((_aa.threshold.value - min) / range)
- * _aa.graphHeight);
+ y2 = (int) (y
+ - ((_aa.threshold.value - min) / range) * _aa.graphHeight);
g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
g2.setStroke(new BasicStroke());
}
}
// calculate where this column extends to in pixels
- int endCol = Math.min(
- Math.round((colIndex + 1) * pixelsPerCol) - 1,
+ int endCol = Math.min(Math.round((colIndex + 1) * pixelsPerCol) - 1,
miniMe.getWidth() - 1);
// don't do expensive colour determination if we're not going to use it
}
else
{
- int endCol = Math.min(
- Math.round((colIndex + 1) * pixelsPerCol) - 1,
+ int endCol = Math.min(Math.round((colIndex + 1) * pixelsPerCol) - 1,
miniMe.getWidth() - 1);
if (annotations[alignmentCol] != null)
g.setColor(annotations[alignmentCol].colour);
}
- height = (int) ((annotations[alignmentCol].value / anno.graphMax) * y);
+ height = (int) ((annotations[alignmentCol].value / anno.graphMax)
+ * y);
if (height > y)
{
height = y;
* the factors that may influence residue colouring are
* <ul>
* <li>the colour scheme that provides a colour for each aligned residue</li>
- * <li>any threshold for colour, based on percentage identity with consensus</li>
+ * <li>any threshold for colour, based on percentage identity with
+ * consensus</li>
* <li>any graduation based on conservation of physico-chemical properties</li>
* </ul>
*
conservation = cons.getConsSequence().getSequenceAsString()
.toCharArray();
}
-
+
}
/**
* get 'base' colour
*/
ProfileI profile = consensus == null ? null : consensus.get(position);
- String modalResidue = profile == null ? null : profile
- .getModalResidue();
- float pid = profile == null ? 0f : profile
- .getPercentageIdentity(ignoreGaps);
- Color colour = colourScheme == null ? Color.white : colourScheme
- .findColour(symbol, position, seq, modalResidue, pid);
+ String modalResidue = profile == null ? null
+ : profile.getModalResidue();
+ float pid = profile == null ? 0f
+ : profile.getPercentageIdentity(ignoreGaps);
+ Color colour = colourScheme == null ? Color.white
+ : colourScheme.findColour(symbol, position, seq, modalResidue,
+ pid);
/*
* apply PID threshold and consensus fading if in force
{
colour = Color.white;
}
-
+
if (conservationColouring)
{
colour = applyConservation(colour, column);
// Faster than toUpperCase
residue -= ('a' - 'A');
}
-
+
if (consensus == null)
{
return false;
}
-
+
ProfileI profile = consensus.get(column);
-
+
/*
* test whether this is the consensus (or joint consensus) residue
*/
return true;
}
}
-
+
return false;
}
return currentColour;
}
char conservationScore = conservation[column];
-
+
/*
* if residues are fully conserved (* or 11), or all properties
* are conserved (+ or 10), leave colour unchanged
{
return currentColour;
}
-
+
if (Comparison.isGap(conservationScore))
{
return Color.white;
}
-
+
/*
* convert score 0-9 to a bleaching factor 1.1 - 0.2
*/
float bleachFactor = (11 - (conservationScore - '0')) / 10f;
-
+
/*
* scale this up by 0-5 (percentage slider / 20)
* as a result, scores of: 0 1 2 3 4 5 6 7 8 9
* fade to white at slider value: 18 20 22 25 29 33 40 50 67 100%
*/
bleachFactor *= (conservationIncrement / 20f);
-
+
return ColorUtils.bleachColour(currentColour, bleachFactor);
}
* @param seq
* @return
*/
- public abstract Color findColour(char symbol, int position, SequenceI seq);
+ public abstract Color findColour(char symbol, int position,
+ SequenceI seq);
public abstract ColourSchemeI getColourScheme();
g.setColor(featureColour);
- g.fillRect((i - start) * charWidth, y1, charWidth,
- charHeight);
+ g.fillRect((i - start) * charWidth, y1, charWidth, charHeight);
if (colourOnly || !validCharWidth)
{
g.setColor(Color.white);
int charOffset = (charWidth - fm.charWidth(s)) / 2;
- g.drawString(String.valueOf(s), charOffset
- + (charWidth * (i - start)), pady);
+ g.drawString(String.valueOf(s),
+ charOffset + (charWidth * (i - start)), pady);
}
return true;
}
g.setColor(Color.black);
int charOffset = (charWidth - fm.charWidth(s)) / 2;
- g.drawString(String.valueOf(s), charOffset
- + (charWidth * (i - start)), pady);
+ g.drawString(String.valueOf(s),
+ charOffset + (charWidth * (i - start)), pady);
}
return true;
}
protected boolean featureGroupNotShown(
final SequenceFeature sequenceFeature)
{
- return featureGroups != null
- && sequenceFeature.featureGroup != null
+ return featureGroups != null && sequenceFeature.featureGroup != null
&& sequenceFeature.featureGroup.length() != 0
&& featureGroups.containsKey(sequenceFeature.featureGroup)
&& !featureGroups.get(sequenceFeature.featureGroup)
{
return null;
}
-
+
/*
* check for new feature added while processing
*/
* inspect features in reverse renderOrder (the last in the array is
* displayed on top) until we find one that is rendered at the position
*/
- for (int renderIndex = renderOrder.length - 1; renderIndex >= 0; renderIndex--)
+ for (int renderIndex = renderOrder.length
+ - 1; renderIndex >= 0; renderIndex--)
{
String type = renderOrder[renderIndex];
if (!showFeatureOfType(type))
}
}
}
-
+
/*
* no displayed feature found at position
*/
seqannot = new IdentityHashMap<SequenceI, AlignmentAnnotation>();
}
// resolve the context containing all the annotation for the sequence
- AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment
+ AnnotatedCollectionI alcontext = alignment instanceof AlignmentI
+ ? alignment
: alignment.getContext();
boolean f = true, rna = false;
- for (AlignmentAnnotation alan : alcontext.findAnnotation(annotation
- .getCalcId()))
+ for (AlignmentAnnotation alan : alcontext
+ .findAnnotation(annotation.getCalcId()))
{
if (alan.sequenceRef != null
- && (alan.label != null && annotation != null && alan.label
- .equals(annotation.label)))
+ && (alan.label != null && annotation != null
+ && alan.label.equals(annotation.label)))
{
if (!rna && alan.isRNA())
{
public Color getMaxColour()
{
- return new Color(redMin + redRange, greenMin + greenRange, blueMin
- + blueRange);
+ return new Color(redMin + redRange, greenMin + greenRange,
+ blueMin + blueRange);
}
/**
/*
* locate the annotation we are configured to colour by
*/
- AlignmentAnnotation ann = (seqAssociated && seqannot != null ? seqannot
- .get(seq) : this.annotation);
+ AlignmentAnnotation ann = (seqAssociated && seqannot != null
+ ? seqannot.get(seq)
+ : this.annotation);
/*
* if gap or no annotation at position, no colour (White)
*/
if (annotationThreshold != null)
{
- if ((aboveAnnotationThreshold == ABOVE_THRESHOLD && aj.value < annotationThreshold.value)
- || (aboveAnnotationThreshold == BELOW_THRESHOLD && aj.value > annotationThreshold.value))
+ if ((aboveAnnotationThreshold == ABOVE_THRESHOLD
+ && aj.value < annotationThreshold.value)
+ || (aboveAnnotationThreshold == BELOW_THRESHOLD
+ && aj.value > annotationThreshold.value))
{
return Color.white;
}
}
else
{
- result = ann.annotations[j].secondaryStructure == 'H' ? AnnotationRenderer.HELIX_COLOUR
- : ann.annotations[j].secondaryStructure == 'E' ? AnnotationRenderer.SHEET_COLOUR
+ result = ann.annotations[j].secondaryStructure == 'H'
+ ? AnnotationRenderer.HELIX_COLOUR
+ : ann.annotations[j].secondaryStructure == 'E'
+ ? AnnotationRenderer.SHEET_COLOUR
: AnnotationRenderer.STEM_COLOUR;
}
}
public class Blosum62ColourScheme extends ResidueColourScheme
{
private static final Color LIGHT_BLUE = new Color(204, 204, 255);
+
private static final Color DARK_BLUE = new Color(154, 154, 255);
public Blosum62ColourScheme()
{
RED(0.9f, 0.2f, 0.1f), BLUE(0.5f, 0.7f, 0.9f), GREEN(0.1f, 0.8f, 0.1f),
ORANGE(0.9f, 0.6f, 0.3f), CYAN(0.1f, 0.7f, 0.7f),
- PINK(0.9f, 0.5f, 0.5f), MAGENTA(0.8f, 0.3f, 0.8f), YELLOW(0.8f, 0.8f,
- 0.0f);
+ PINK(0.9f, 0.5f, 0.5f), MAGENTA(0.8f, 0.3f, 0.8f),
+ YELLOW(0.8f, 0.8f, 0.0f);
final Color colour;
colour = new Color(r, g, b);
}
}
+
private class ConsensusColour
{
Consensus[] cons;
for (int k = 0; k < residueColour[i].cons.length; k++)
{
- if (residueColour[i].cons[k].isConserved(cons2, j, size,
- includeGaps))
+ if (residueColour[i].cons[k].isConserved(cons2, j, size, includeGaps))
{
colour = residueColour[i].c;
}
{
InputStreamReader in = new InputStreamReader(
new FileInputStream(file), "UTF-8");
-
+
jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours();
-
+
org.exolab.castor.xml.Unmarshaller unmar = new org.exolab.castor.xml.Unmarshaller(
jucs);
jucs = (jalview.schemabinding.version2.JalviewUserColours) unmar
.unmarshal(in);
-
+
/*
* non-case-sensitive colours are for 20 amino acid codes,
* B, Z, X and Gap
newColours = new Color[24];
Color[] lowerCase = new Color[23];
boolean caseSensitive = false;
-
+
String name;
int index;
for (int i = 0; i < jucs.getColourCount(); i++)
{
continue;
}
-
- Color color = new Color(Integer.parseInt(jucs.getColour(i)
- .getRGB(), 16));
+
+ Color color = new Color(
+ Integer.parseInt(jucs.getColour(i).getRGB(), 16));
if (name.toLowerCase().equals(name))
{
caseSensitive = true;
newColours[index] = color;
}
}
-
+
/*
* instantiate the colour scheme
*/
// Could be old Jalview Archive format
try
{
- InputStreamReader in = new InputStreamReader(new FileInputStream(
- file), "UTF-8");
-
+ InputStreamReader in = new InputStreamReader(
+ new FileInputStream(file), "UTF-8");
+
jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours();
-
+
jucs = JalviewUserColours.unmarshal(in);
-
+
newColours = new Color[jucs.getColourCount()];
-
+
for (int i = 0; i < 24; i++)
{
- newColours[i] = new Color(Integer.parseInt(jucs.getColour(i)
- .getRGB(), 16));
+ newColours[i] = new Color(
+ Integer.parseInt(jucs.getColour(i).getRGB(), 16));
}
ucs = new UserColourScheme(newColours);
ucs.setName(jucs.getSchemeName());
{
ex2.printStackTrace();
}
-
+
if (newColours == null)
{
System.out.println("Error loading User ColourFile\n" + ex);
}
}
-
+
return ucs;
}
* Returns a colour scheme for the given name, with which the given data may
* be coloured. The name is not case-sensitive, and may be one of
* <ul>
- * <li>any currently registered colour scheme; Jalview by default provides</li>
+ * <li>any currently registered colour scheme; Jalview by default
+ * provides</li>
* <ul>
* <li>Clustal</li>
* <li>Blosum62</li>
* <li>T-Coffee Scores</li>
* <li>RNA Helices</li>
* </ul>
- * <li>the name of a programmatically added colour scheme</li> <li>an AWT
- * colour name e.g. red</li> <li>an AWT hex rgb colour e.g. ff2288</li> <li>
- * residue colours list e.g. D,E=red;K,R,H=0022FF;c=yellow</li> </ul>
+ * <li>the name of a programmatically added colour scheme</li>
+ * <li>an AWT colour name e.g. red</li>
+ * <li>an AWT hex rgb colour e.g. ff2288</li>
+ * <li>residue colours list e.g. D,E=red;K,R,H=0022FF;c=yellow</li>
+ * </ul>
*
* If none of these formats is matched, the string is converted to a colour
* using a hashing algorithm. For name "None", returns null.
* if this is the name of a registered colour scheme, just
* create a new instance of it
*/
- ColourSchemeI scheme = ColourSchemes.getInstance().getColourScheme(
- name, forData, null);
+ ColourSchemeI scheme = ColourSchemes.getInstance().getColourScheme(name,
+ forData, null);
if (scheme != null)
{
return scheme;
*/
public static String getColourName(ColourSchemeI cs)
{
- return cs == null ? ResidueColourScheme.NONE : cs
- .getSchemeName();
+ return cs == null ? ResidueColourScheme.NONE : cs.getSchemeName();
}
}
schemes.remove(name.toLowerCase());
}
}
-
+
/**
* Returns an instance of the colour scheme with which the given view may be
* coloured
positionsToHelix.put(this.annotation._rnasecstr[x].getEnd(),
this.annotation._rnasecstr[x].getFeatureGroup());
- if (Integer.parseInt(this.annotation._rnasecstr[x].getFeatureGroup()) > numHelix)
+ if (Integer.parseInt(
+ this.annotation._rnasecstr[x].getFeatureGroup()) > numHelix)
{
- numHelix = Integer.parseInt(this.annotation._rnasecstr[x]
- .getFeatureGroup());
+ numHelix = Integer
+ .parseInt(this.annotation._rnasecstr[x].getFeatureGroup());
}
}
Color colour = ColorUtils.parseColourString(descriptor);
if (colour == null)
{
- throw new IllegalArgumentException("Invalid colour descriptor: "
- + descriptor);
+ throw new IllegalArgumentException(
+ "Invalid colour descriptor: " + descriptor);
}
return new FeatureColour(colour);
}
{
if (!ttype.toLowerCase().startsWith("no"))
{
- System.err.println("Ignoring unrecognised threshold type : "
- + ttype);
+ System.err.println(
+ "Ignoring unrecognised threshold type : " + ttype);
}
}
}
}
if (gcol.hasMoreTokens())
{
- System.err
- .println("Ignoring additional tokens in parameters in graduated colour specification\n");
+ System.err.println(
+ "Ignoring additional tokens in parameters in graduated colour specification\n");
while (gcol.hasMoreTokens())
{
System.err.println("|" + gcol.nextToken());
{
if (isColourByLabel())
{
- return ColorUtils
- .createColourFromName(feature.getDescription());
+ return ColorUtils.createColourFromName(feature.getDescription());
}
if (!isGraduatedColour())
package jalview.schemes;
-
/**
* An enum with the colour schemes supported by Jalview.
*/
* the order of declaration is the default order in which
* items are added to Colour menus
*/
- Clustal("Clustal", ClustalxColourScheme.class), Blosum62("Blosum62",
- Blosum62ColourScheme.class), PID("% Identity",
- PIDColourScheme.class), Zappo("Zappo", ZappoColourScheme.class),
- Taylor("Taylor", TaylorColourScheme.class), Hydrophobic("Hydrophobic",
- HydrophobicColourScheme.class), Helix("Helix Propensity",
- HelixColourScheme.class), Strand("Strand Propensity",
- StrandColourScheme.class), Turn("Turn Propensity",
- TurnColourScheme.class), Buried("Buried Index",
- BuriedColourScheme.class), Nucleotide("Nucleotide",
- NucleotideColourScheme.class), PurinePyrimidine(
- "Purine/Pyrimidine", PurinePyrimidineColourScheme.class),
- RNAHelices("RNA Helices", RNAHelicesColour.class), TCoffee(
- "T-Coffee Scores", TCoffeeColourScheme.class);
+ Clustal("Clustal", ClustalxColourScheme.class),
+ Blosum62("Blosum62", Blosum62ColourScheme.class),
+ PID("% Identity", PIDColourScheme.class),
+ Zappo("Zappo", ZappoColourScheme.class),
+ Taylor("Taylor", TaylorColourScheme.class),
+ Hydrophobic("Hydrophobic", HydrophobicColourScheme.class),
+ Helix("Helix Propensity", HelixColourScheme.class),
+ Strand("Strand Propensity", StrandColourScheme.class),
+ Turn("Turn Propensity", TurnColourScheme.class),
+ Buried("Buried Index", BuriedColourScheme.class),
+ Nucleotide("Nucleotide", NucleotideColourScheme.class),
+ PurinePyrimidine("Purine/Pyrimidine", PurinePyrimidineColourScheme.class),
+ RNAHelices("RNA Helices", RNAHelicesColour.class),
+ TCoffee("T-Coffee Scores", TCoffeeColourScheme.class);
// RNAInteraction("RNA Interaction type", RNAInteractionColourScheme.class)
private String name;
/*
* test whether this is the consensus (or joint consensus) residue
*/
- boolean matchesConsensus = consensusResidue.contains(
- String.valueOf(c));
+ boolean matchesConsensus = consensusResidue.contains(String.valueOf(c));
if (matchesConsensus)
{
for (int i = 0; i < thresholds.length; i++)
public void refresh()
{
- if (annotation != null
- && ((annotation._rnasecstr == null || lastrefresh != annotation._rnasecstr
- .hashCode()) && annotation.isValidStruc()))
+ if (annotation != null && ((annotation._rnasecstr == null
+ || lastrefresh != annotation._rnasecstr.hashCode())
+ && annotation.isValidStruc()))
{
annotation.getRNAStruc();
lastrefresh = annotation._rnasecstr.hashCode();
positionsToHelix.put(this.annotation._rnasecstr[x].getEnd(),
this.annotation._rnasecstr[x].getFeatureGroup());
- if (Integer.parseInt(this.annotation._rnasecstr[x]
- .getFeatureGroup()) > numHelix)
+ if (Integer.parseInt(
+ this.annotation._rnasecstr[x].getFeatureGroup()) > numHelix)
{
- numHelix = Integer.parseInt(this.annotation._rnasecstr[x]
- .getFeatureGroup());
+ numHelix = Integer.parseInt(
+ this.annotation._rnasecstr[x].getFeatureGroup());
}
}
/**
* Creates a new ResidueColourScheme object.
*
- * @param final int[] index table into colors (ResidueProperties.naIndex or
- * ResidueProperties.aaIndex)
+ * @param final
+ * int[] index table into colors (ResidueProperties.naIndex or
+ * ResidueProperties.aaIndex)
* @param colors
* colours for symbols in sequences
*/
{
Color colour = Color.white;
- if (colors != null && symbolIndex != null
- && c < symbolIndex.length
+ if (colors != null && symbolIndex != null && c < symbolIndex.length
&& symbolIndex[c] < colors.length)
{
colour = colors[symbolIndex[c]];
};
// Added for PurinePyrimidineColourScheme
- public static final Color[] purinepyrimidine = {
- new Color(255, 131, 250), // A, G, R purines purplish/orchid
+ public static final Color[] purinepyrimidine = { new Color(255, 131, 250), // A,
+ // G,
+ // R
+ // purines
+ // purplish/orchid
new Color(64, 224, 208), // C,U, T, Y pyrimidines turquoise
Color.white, // all other nucleotides
Color.white // Gap
Color.green, // Q
Color.red, // E
Color.magenta, // G
- midBlue,// Color.red, // H
+ midBlue, // Color.red, // H
Color.pink, // I
Color.pink, // L
midBlue, // K
0.0 // X
};
- public static final double[] helix = { 1.42, 0.98, 0.67, 1.01, 0.70,
- 1.11, 1.51, 0.57, 1.00, 1.08, 1.21, 1.16, 1.45, 1.13, 0.57, 0.77,
- 0.83, 1.08, 0.69, 1.06, 0.84, 1.31, 1.00, 0.0 };
+ public static final double[] helix = { 1.42, 0.98, 0.67, 1.01, 0.70, 1.11,
+ 1.51, 0.57, 1.00, 1.08, 1.21, 1.16, 1.45, 1.13, 0.57, 0.77, 0.83,
+ 1.08, 0.69, 1.06, 0.84, 1.31, 1.00, 0.0 };
public static final double helixmin = 0.57;
public static final double turnmax = 1.56;
- public static final double[] buried = { 1.7, 0.1, 0.4, 0.4, 4.6, 0.3,
- 0.3, 1.8, 0.8, 3.1, 2.4, 0.05, 1.9, 2.2, 0.6, 0.8, 0.7, 1.6, 0.5,
- 2.9, 0.4, 0.3, 1.358, 0.00 };
+ public static final double[] buried = { 1.7, 0.1, 0.4, 0.4, 4.6, 0.3, 0.3,
+ 1.8, 0.8, 3.1, 2.4, 0.05, 1.9, 2.2, 0.6, 0.8, 0.7, 1.6, 0.5, 2.9, 0.4,
+ 0.3, 1.358, 0.00 };
public static final double buriedmin = 0.05;
}
else
{
- System.err
- .println("Inconsistency in the IUBMB ambiguity code nomenclature table: collision for "
+ System.err.println(
+ "Inconsistency in the IUBMB ambiguity code nomenclature table: collision for "
+ acode.getKey() + " in residue " + r);
}
}
}
// and programmatically add in the ambiguity codes that yield the same amino
// acid
- String[] unambcodons = codonHash2.keySet().toArray(
- new String[codonHash2.size()]);
+ String[] unambcodons = codonHash2.keySet()
+ .toArray(new String[codonHash2.size()]);
for (String codon : unambcodons)
{
String residue = codonHash2.get(codon);
}
}
// enumerate all combinations and test for veracity of translation
- int tpos[] = new int[codon.length()], cpos[] = new int[codon.length()];
+ int tpos[] = new int[codon.length()],
+ cpos[] = new int[codon.length()];
for (int i = 0; i < tpos.length; i++)
{
tpos[i] = -1;
charged.put("Q", ZERO);
charged.put("D", ONE);
charged.put("N", ZERO); // Asparagine is polar but not
- // charged.
+ // charged.
// Alternative would be charged and
// negative (in basic form)?
charged.put("S", ZERO);
}
static
{
- int[][] propMatrixF = new int[maxProteinIndex][maxProteinIndex], propMatrixPos = new int[maxProteinIndex][maxProteinIndex], propMatrixEpos = new int[maxProteinIndex][maxProteinIndex];
+ int[][] propMatrixF = new int[maxProteinIndex][maxProteinIndex],
+ propMatrixPos = new int[maxProteinIndex][maxProteinIndex],
+ propMatrixEpos = new int[maxProteinIndex][maxProteinIndex];
for (int i = 0; i < maxProteinIndex; i++)
{
int maxF = 0, maxP = 0, maxEP = 0;
{
return '0';
}
- Integer index = ResidueProperties.aa3Hash.get(threeLetterCode
- .toUpperCase());
+ Integer index = ResidueProperties.aa3Hash
+ .get(threeLetterCode.toUpperCase());
return index == null ? '0' : aa[index].charAt(0);
}
}
// Search alignment to get all tcoffee annotation and pick one set of
// annotation to use to colour seqs.
seqMap = new IdentityHashMap<SequenceI, Color[]>();
- AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment
+ AnnotatedCollectionI alcontext = alignment instanceof AlignmentI
+ ? alignment
: alignment.getContext();
if (alcontext == null)
{
@Override
public boolean isApplicableTo(AnnotatedCollectionI ac)
{
- AnnotatedCollectionI alcontext = ac instanceof AlignmentI ? ac : ac
- .getContext();
+ AnnotatedCollectionI alcontext = ac instanceof AlignmentI ? ac
+ : ac.getContext();
if (alcontext == null)
{
return false;
{
lowerCaseColours = new Color[colors.length];
}
- lowerCaseColours[colIndex] = ColorUtils.parseColourString(colour);
+ lowerCaseColours[colIndex] = ColorUtils
+ .parseColourString(colour);
}
else
{
}
} catch (Exception ex)
{
- System.out.println("Error parsing userDefinedColours:\n" + token
- + "\n" + ex);
+ System.out.println(
+ "Error parsing userDefinedColours:\n" + token + "\n" + ex);
}
}
}
/**
- * Answers the customised name of the colour scheme, if it has one, else
- * "User Defined"
+ * Answers the customised name of the colour scheme, if it has one, else "User
+ * Defined"
*/
@Override
public String getSchemeName()
* @param position
* the dataset sequence position (base 1)
*/
- public void mouseOverSequence(SequenceI sequence, int index, int position);
+ public void mouseOverSequence(SequenceI sequence, int index,
+ int position);
}
*/
public void selection(jalview.datamodel.SequenceGroup seqsel,
jalview.datamodel.ColumnSelection colsel,
- jalview.datamodel.HiddenColumns hidden,
- SelectionSource source);
+ jalview.datamodel.HiddenColumns hidden, SelectionSource source);
}
}
else
{
- System.err.println("reportMapping: There are " + mappings.size()
- + " mappings.");
+ System.err.println(
+ "reportMapping: There are " + mappings.size() + " mappings.");
int i = 0;
for (StructureMapping sm : mappings)
{
{
if (instances != null)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_structure_selection_manager_null"),
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_structure_selection_manager_null"),
new NullPointerException(MessageManager
.getString("exception.ssm_context_is_null")));
}
}
else if (seq.getName().indexOf("|") > -1)
{
- targetChainId = seq.getName().substring(
- seq.getName().lastIndexOf("|") + 1);
+ targetChainId = seq.getName()
+ .substring(seq.getName().lastIndexOf("|") + 1);
if (targetChainId.length() > 1)
{
if (targetChainId.trim().length() == 0)
setProgressBar(null);
setProgressBar(MessageManager
.getString("status.obtaining_mapping_with_nw_alignment"));
- StructureMapping nwMapping = getNWMappings(seq, pdbFile,
- maxChainId, maxChain, pdb, maxAlignseq);
+ StructureMapping nwMapping = getNWMappings(seq, pdbFile, maxChainId,
+ maxChain, pdb, maxAlignseq);
seqToStrucMapping.add(nwMapping);
ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
AlignSeq maxAlignseq)
{
final StringBuilder mappingDetails = new StringBuilder(128);
- mappingDetails.append(NEWLINE).append(
- "Sequence \u27f7 Structure mapping details");
+ mappingDetails.append(NEWLINE)
+ .append("Sequence \u27f7 Structure mapping details");
mappingDetails.append(NEWLINE);
mappingDetails
.append("Method: inferred with Needleman & Wunsch alignment");
.append(" ");
mappingDetails.append(String.valueOf(maxAlignseq.seq2end));
mappingDetails.append(NEWLINE).append("SEQ start/end ");
- mappingDetails.append(
- String.valueOf(maxAlignseq.seq1start + (seq.getStart() - 1)))
+ mappingDetails
+ .append(String
+ .valueOf(maxAlignseq.seq1start + (seq.getStart() - 1)))
.append(" ");
- mappingDetails.append(String.valueOf(maxAlignseq.seq1end
- + (seq.getStart() - 1)));
+ mappingDetails.append(
+ String.valueOf(maxAlignseq.seq1end + (seq.getStart() - 1)));
mappingDetails.append(NEWLINE);
maxChain.makeExactMapping(maxAlignseq, seq);
jalview.datamodel.Mapping sqmpping = maxAlignseq
insCode = tmp.insCode;
if (tmp.alignmentMapping >= -1)
{
- mapping.put(tmp.alignmentMapping + 1, new int[] { tmp.resNumber,
- tmp.atomIndex });
+ mapping.put(tmp.alignmentMapping + 1,
+ new int[]
+ { tmp.resNumber, tmp.atomIndex });
}
}
* @param chain
* @param pdbfile
*/
- public void mouseOverStructure(int pdbResNum, String chain, String pdbfile)
+ public void mouseOverStructure(int pdbResNum, String chain,
+ String pdbfile)
{
AtomSpec atomSpec = new AtomSpec(pdbfile, chain, pdbResNum, 0);
List<AtomSpec> atoms = Collections.singletonList(atomSpec);
return;
}
- SearchResultsI results = findAlignmentPositionsForStructurePositions(atoms);
+ SearchResultsI results = findAlignmentPositionsForStructurePositions(
+ atoms);
for (Object li : listeners)
{
if (li instanceof SequenceListener)
List<AtomSpec> atoms = new ArrayList<AtomSpec>();
for (StructureMapping sm : mappings)
{
- if (sm.sequence == seq
- || sm.sequence == seq.getDatasetSequence()
+ if (sm.sequence == seq || sm.sequence == seq.getDatasetSequence()
|| (sm.sequence.getDatasetSequence() != null && sm.sequence
.getDatasetSequence() == seq.getDatasetSequence()))
{
if (atomNo > 0)
{
- atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain, sm
- .getPDBResNum(index), atomNo));
+ atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain,
+ sm.getPDBResNum(index), atomNo));
}
}
}
{
if (command instanceof EditCommand)
{
- return MappingUtils.mapEditCommand((EditCommand) command, undo,
- mapTo, gapChar, seqmappings);
+ return MappingUtils.mapEditCommand((EditCommand) command, undo, mapTo,
+ gapChar, seqmappings);
}
else if (command instanceof OrderCommand)
{
* @author gmcarstairs
*
*/
-public abstract class AAStructureBindingModel extends
- SequenceStructureBindingModel implements StructureListener,
- StructureSelectionManagerProvider
+public abstract class AAStructureBindingModel
+ extends SequenceStructureBindingModel
+ implements StructureListener, StructureSelectionManagerProvider
{
private StructureSelectionManager ssm;
{
throw new Error(MessageManager.formatMessage(
"error.implementation_error_no_pdbentry_from_index",
- new Object[] { Integer.valueOf(pe).toString() }));
+ new Object[]
+ { Integer.valueOf(pe).toString() }));
}
final String nullChain = "TheNullChain";
List<SequenceI> s = new ArrayList<SequenceI>();
if (waiting)
{
- System.err
- .println("Timed out waiting for structure viewer to load file "
+ System.err.println(
+ "Timed out waiting for structure viewer to load file "
+ notLoaded);
return false;
}
{
for (SequenceI s : seqs)
{
- if (s == seq
- || (s.getDatasetSequence() != null && s
- .getDatasetSequence() == seq
- .getDatasetSequence()))
+ if (s == seq || (s.getDatasetSequence() != null
+ && s.getDatasetSequence() == seq.getDatasetSequence()))
{
return true;
}
*
* @return
*/
- public abstract SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment);
+ public abstract SequenceRenderer getSequenceRenderer(
+ AlignmentViewPanel alignment);
protected abstract void colourBySequence(
StructureMappingcommandSet[] colourBySequenceCommands);
return;
}
String[] files = getStructureFiles();
-
+
SequenceRenderer sr = getSequenceRenderer(alignmentv);
-
+
StructureMappingcommandSet[] colourBySequenceCommands = getColourBySequenceCommands(
files, sr, alignmentv);
colourBySequence(colourBySequenceCommands);
import jalview.api.SequenceStructureBinding;
-public class SequenceStructureBindingModel implements
- SequenceStructureBinding
+public class SequenceStructureBindingModel
+ implements SequenceStructureBinding
{
/**
{
Map.Entry<String, String> pair = it.next();
urls.put(pair.getKey(),
- new UrlLink(pair.getKey(), pair.getValue(),
- pair.getKey()));
+ new UrlLink(pair.getKey(), pair.getValue(), pair.getKey()));
}
upgradeOldLinks(urls);
return urls;
}
if (link.getIsSelected())
{
- selurls.put(link.getId(),
- new UrlLink(link.getDescription(), link.getUrl(), link.getDescription()));
+ selurls.put(link.getId(), new UrlLink(link.getDescription(),
+ link.getUrl(), link.getDescription()));
}
else
{
- unselurls
- .put(link.getId(),
- new UrlLink(link.getDescription(), link.getUrl(), link
- .getDescription()));
+ unselurls.put(link.getId(), new UrlLink(link.getDescription(),
+ link.getUrl(), link.getDescription()));
}
// sort out primary and selected ids
if (link.getIsPrimary())
@Override
public boolean contains(String id)
{
- return (selectedUrls.containsKey(id) || nonselectedUrls.containsKey(id));
+ return (selectedUrls.containsKey(id)
+ || nonselectedUrls.containsKey(id));
}
}
* name of identifiers.org download file
* @return hashmap of identifiers.org data, keyed by MIRIAM id
*/
- private HashMap<String, UrlLink> readIdentifiers(
- String idFileName)
+ private HashMap<String, UrlLink> readIdentifiers(String idFileName)
{
JSONParser parser = new JSONParser();
}
else
{
- System.out
- .println("Unexpected key returned from identifiers jalview service");
+ System.out.println(
+ "Unexpected key returned from identifiers jalview service");
return idData;
}
private UrlLink link;
- public UrlLinkDisplay(String rowId, UrlLink rowLink,
- boolean rowSelected, boolean rowDefault)
+ public UrlLinkDisplay(String rowId, UrlLink rowLink, boolean rowSelected,
+ boolean rowDefault)
{
id = rowId;
isPrimary = rowDefault;
public boolean isRowDeletable(int rowIndex)
{
// to delete, row must be a user entered row, and not the default row
- return (dataProvider.isUserEntry(data.get(rowIndex).getId()) && !data
- .get(rowIndex).getIsPrimary());
+ return (dataProvider.isUserEntry(data.get(rowIndex).getId())
+ && !data.get(rowIndex).getIsPrimary());
}
@Override
}
}
- System.out
- .println("Error initialising UrlProvider - no custom url provider");
+ System.out.println(
+ "Error initialising UrlProvider - no custom url provider");
return null;
}
-
+
@Override
public boolean setPrimaryUrl(String id)
{
}
return outcome;
}
-
+
@Override
public String writeUrlsAsString(boolean selected)
{
}
return target;
}
-
+
@Override
public String choosePrimaryUrl()
{
protected String primaryUrl;
- protected String getPrimaryUrl(String seqid, HashMap<String, UrlLink> urls)
+ protected String getPrimaryUrl(String seqid,
+ HashMap<String, UrlLink> urls)
{
if (seqid.length() < MIN_SUBST_LENGTH)
{
{
isSelected = selected;
}
- displayLinks.add(new UrlLinkDisplay(key, entry.getValue(),
- isSelected, isPrimary));
+ displayLinks.add(new UrlLinkDisplay(key, entry.getValue(), isSelected,
+ isPrimary));
}
return displayLinks;
}
return !isMiriamId(id);
}
}
-
*/
package jalview.urls.api;
-
/**
* Interface to UrlProvider factories
*
import java.io.PipedOutputStream;
import java.io.PrintStream;
-public class AWTConsole extends WindowAdapter implements WindowListener,
- ActionListener, Runnable
+public class AWTConsole extends WindowAdapter
+ implements WindowListener, ActionListener, Runnable
{
private Frame frame;
* functionality or any adverse or unexpected effects of using this software.
* <p>
* Credits: <br>
- * Steven Spencer, JavaWorld magazine (<a
- * href="http://www.javaworld.com/javaworld/javatips/jw-javatip66.html">Java Tip
- * 66</a>) <br>
+ * Steven Spencer, JavaWorld magazine
+ * (<a href="http://www.javaworld.com/javaworld/javatips/jw-javatip66.html">Java
+ * Tip 66</a>) <br>
* Thanks also to Ron B. Yeh, Eric Shapiro, Ben Engber, Paul Teitlebaum, Andrea
* Cantatore, Larry Barowski, Trevor Bedzek, Frank Miedrich, and Ron Rabakukk
*
- * @author Eric Albert (<a
- * href="mailto:ejalbert@cs.stanford.edu">ejalbert@cs.stanford.edu</a>)
+ * @author Eric Albert (<a href=
+ * "mailto:ejalbert@cs.stanford.edu">ejalbert@cs.stanford.edu</a>)
* @version 1.4b1 (Released June 20, 2001)
*/
public class BrowserLauncher
aeDescClass = Class.forName("com.apple.MacOS.AEDesc");
aeTargetConstructor = aeTargetClass
- .getDeclaredConstructor(new Class[] { int.class });
+ .getDeclaredConstructor(new Class[]
+ { int.class });
appleEventConstructor = appleEventClass
- .getDeclaredConstructor(new Class[] { int.class, int.class,
- aeTargetClass, int.class, int.class });
+ .getDeclaredConstructor(new Class[]
+ { int.class, int.class, aeTargetClass, int.class,
+ int.class });
aeDescConstructor = aeDescClass
- .getDeclaredConstructor(new Class[] { String.class });
+ .getDeclaredConstructor(new Class[]
+ { String.class });
makeOSType = osUtilsClass.getDeclaredMethod("makeOSType",
- new Class[] { String.class });
+ new Class[]
+ { String.class });
putParameter = appleEventClass.getDeclaredMethod("putParameter",
- new Class[] { int.class, aeDescClass });
+ new Class[]
+ { int.class, aeDescClass });
sendNoReply = appleEventClass.getDeclaredMethod("sendNoReply",
new Class[] {});
.getDeclaredField("kSystemFolderType");
kSystemFolderType = systemFolderField.get(null);
findFolder = mrjFileUtilsClass.getDeclaredMethod("findFolder",
- new Class[] { mrjOSTypeClass });
- getFileCreator = mrjFileUtilsClass.getDeclaredMethod(
- "getFileCreator", new Class[] { File.class });
+ new Class[]
+ { mrjOSTypeClass });
+ getFileCreator = mrjFileUtilsClass
+ .getDeclaredMethod("getFileCreator", new Class[]
+ { File.class });
getFileType = mrjFileUtilsClass.getDeclaredMethod("getFileType",
- new Class[] { File.class });
+ new Class[]
+ { File.class });
} catch (ClassNotFoundException cnfe)
{
errorMessage = cnfe.getMessage();
{
Class linker = Class.forName("com.apple.mrj.jdirect.Linker");
Constructor constructor = linker
- .getConstructor(new Class[] { Class.class });
+ .getConstructor(new Class[]
+ { Class.class });
linkage = constructor
- .newInstance(new Object[] { BrowserLauncher.class });
+ .newInstance(new Object[]
+ { BrowserLauncher.class });
} catch (ClassNotFoundException cnfe)
{
errorMessage = cnfe.getMessage();
{
mrjFileUtilsClass = Class.forName("com.apple.mrj.MRJFileUtils");
openURL = mrjFileUtilsClass.getDeclaredMethod("openURL",
- new Class[] { String.class });
+ new Class[]
+ { String.class });
} catch (ClassNotFoundException cnfe)
{
errorMessage = cnfe.getMessage();
try
{
Integer finderCreatorCode = (Integer) makeOSType.invoke(null,
- new Object[] { FINDER_CREATOR });
+ new Object[]
+ { FINDER_CREATOR });
Object aeTarget = aeTargetConstructor
- .newInstance(new Object[] { finderCreatorCode });
+ .newInstance(new Object[]
+ { finderCreatorCode });
Integer gurlType = (Integer) makeOSType.invoke(null,
- new Object[] { GURL_EVENT });
- Object appleEvent = appleEventConstructor.newInstance(new Object[] {
- gurlType, gurlType, aeTarget, kAutoGenerateReturnID,
- kAnyTransactionID });
+ new Object[]
+ { GURL_EVENT });
+ Object appleEvent = appleEventConstructor
+ .newInstance(new Object[]
+ { gurlType, gurlType, aeTarget, kAutoGenerateReturnID,
+ kAnyTransactionID });
// Don't set browser = appleEvent because then the next time we call
// locateBrowser(), we'll get the same AppleEvent, to which we'll
try
{
systemFolder = (File) findFolder.invoke(null,
- new Object[] { kSystemFolderType });
+ new Object[]
+ { kSystemFolderType });
} catch (IllegalArgumentException iare)
{
browser = null;
if (FINDER_TYPE.equals(fileType.toString()))
{
Object fileCreator = getFileCreator.invoke(null,
- new Object[] { file });
+ new Object[]
+ { file });
if (FINDER_CREATOR.equals(fileCreator.toString()))
{
{
if (!loadedWithoutErrors)
{
- throw new IOException(MessageManager.formatMessage(
- "exception.browser_not_found", new String[] { errorMessage }));
+ throw new IOException(MessageManager
+ .formatMessage("exception.browser_not_found", new String[]
+ { errorMessage }));
}
Object browser = locateBrowser();
if (browser == null)
{
throw new IOException(MessageManager.formatMessage(
- "exception.browser_unable_to_locate",
- new String[] { errorMessage }));
+ "exception.browser_unable_to_locate", new String[]
+ { errorMessage }));
}
switch (jvm)
{
aeDesc = aeDescConstructor.newInstance(new Object[] { url });
putParameter.invoke(browser,
- new Object[] { keyDirectObject, aeDesc });
+ new Object[]
+ { keyDirectObject, aeDesc });
sendNoReply.invoke(browser, new Object[] {});
} catch (InvocationTargetException ite)
{
throw new IOException(MessageManager.formatMessage(
"exception.invocation_target_exception_creating_aedesc",
- new String[] { ite.getMessage() }));
+ new String[]
+ { ite.getMessage() }));
} catch (IllegalAccessException iae)
{
throw new IOException(MessageManager.formatMessage(
else
{
throw new IOException(MessageManager.formatMessage(
- "exception.unable_to_launch_url", new String[] { Integer
- .valueOf(result).toString() }));
+ "exception.unable_to_launch_url", new String[]
+ { Integer.valueOf(result).toString() }));
}
}
else
{
throw new IOException(MessageManager.formatMessage(
- "exception.unable_to_create_internet_config",
- new String[] { Integer.valueOf(result).toString() }));
+ "exception.unable_to_create_internet_config", new String[]
+ { Integer.valueOf(result).toString() }));
}
break;
} catch (InvocationTargetException ite)
{
throw new IOException(MessageManager.formatMessage(
- "exception.invocation_target_calling_url",
- new String[] { ite.getMessage() }));
+ "exception.invocation_target_calling_url", new String[]
+ { ite.getMessage() }));
} catch (IllegalAccessException iae)
{
throw new IOException(MessageManager.formatMessage(
- "exception.illegal_access_calling_url",
- new String[] { iae.getMessage() }));
+ "exception.illegal_access_calling_url", new String[]
+ { iae.getMessage() }));
}
break;
// Add quotes around the URL to allow ampersands and other special
// characters to work.
- Process process = Runtime.getRuntime().exec(
- new String[] { (String) browser, FIRST_WINDOWS_PARAMETER,
+ Process process = Runtime.getRuntime()
+ .exec(new String[]
+ { (String) browser, FIRST_WINDOWS_PARAMETER,
SECOND_WINDOWS_PARAMETER, THIRD_WINDOWS_PARAMETER,
'"' + url + '"' });
} catch (InterruptedException ie)
{
throw new IOException(MessageManager.formatMessage(
- "exception.interrupted_launching_browser",
- new String[] { ie.getMessage() }));
+ "exception.interrupted_launching_browser", new String[]
+ { ie.getMessage() }));
}
break;
* NETSCAPE_REMOTE_PARAMETER+" "+ NETSCAPE_OPEN_PARAMETER_START + url +
* NETSCAPE_OPEN_NEW_WINDOW + NETSCAPE_OPEN_PARAMETER_END);
*/
- process = Runtime.getRuntime().exec(
- new String[] {
- (String) browser,
- NETSCAPE_REMOTE_PARAMETER,
+ process = Runtime.getRuntime()
+ .exec(new String[]
+ { (String) browser, NETSCAPE_REMOTE_PARAMETER,
NETSCAPE_OPEN_PARAMETER_START + url
+ NETSCAPE_OPEN_NEW_WINDOW
} catch (InterruptedException ie)
{
throw new IOException(MessageManager.formatMessage(
- "exception.interrupted_launching_browser",
- new String[] { ie.getMessage() }));
+ "exception.interrupted_launching_browser", new String[]
+ { ie.getMessage() }));
}
break;
@Override
public int hashCode()
{
- return value == null ? super.hashCode() : value.toUpperCase()
- .hashCode();
+ return value == null ? super.hashCode()
+ : value.toUpperCase().hashCode();
}
}
* prop = proportion of the way value is from minValue to maxValue
*/
float prop = (value - minValue) / (maxValue - minValue);
- float r = minColour.getRed() + prop
- * (maxColour.getRed() - minColour.getRed());
- float g = minColour.getGreen() + prop
- * (maxColour.getGreen() - minColour.getGreen());
- float b = minColour.getBlue() + prop
- * (maxColour.getBlue() - minColour.getBlue());
+ float r = minColour.getRed()
+ + prop * (maxColour.getRed() - minColour.getRed());
+ float g = minColour.getGreen()
+ + prop * (maxColour.getGreen() - minColour.getGreen());
+ float b = minColour.getBlue()
+ + prop * (maxColour.getBlue() - minColour.getBlue());
return new Color(r / 255, g / 255, b / 255);
}
return null;
}
colour = colour.trim();
-
+
Color col = null;
try
{
} catch (NumberFormatException ex)
{
}
-
+
if (col == null)
{
col = ColorUtils.getAWTColorFromName(colour);
}
-
+
if (col == null)
{
try
// non-numeric token or out of 0-255 range
}
}
-
+
return col;
}
int lsize = name.length();
int start = 0;
int end = lsize / 3;
-
+
int rgbOffset = Math.abs(name.hashCode() % 10) * 15; // 0-135
-
+
/*
* red: first third
*/
- int r = Math.abs(name.substring(start, end).hashCode() + rgbOffset) % 210 + 20;
+ int r = Math.abs(name.substring(start, end).hashCode() + rgbOffset)
+ % 210 + 20;
start = end;
end += lsize / 3;
if (end > lsize)
{
end = lsize;
}
-
+
/*
* green: second third
*/
- int g = Math.abs(name.substring(start, end).hashCode() + rgbOffset) % 210 + 20;
-
+ int g = Math.abs(name.substring(start, end).hashCode() + rgbOffset)
+ % 210 + 20;
+
/*
* blue: third third
*/
int b = Math.abs(name.substring(end).hashCode() + rgbOffset) % 210 + 20;
-
+
Color color = new Color(r, g, b);
-
+
return color;
}
}
Color col = null;
name = name.toLowerCase();
-
+
// or make a static map; or use reflection on the field name
switch (name)
{
col = Color.yellow;
break;
}
-
+
return col;
}
}
public static final char GAP_DASH = '-';
- public static final String GapChars = new String(new char[] { GAP_SPACE,
- GAP_DOT, GAP_DASH });
+ public static final String GapChars = new String(
+ new char[]
+ { GAP_SPACE, GAP_DOT, GAP_DASH });
/**
* DOCUMENT ME!
* int
* @return float
*/
- public static float compare(SequenceI ii, SequenceI jj, int start, int end)
+ public static float compare(SequenceI ii, SequenceI jj, int start,
+ int end)
{
String si = ii.getSequenceAsString();
String sj = jj.getSequenceAsString();
{
for (int j = 0; j < jlen; j++)
{
- if (si.substring(start + j, start + j + 1).equals(
- sj.substring(start + j, start + j + 1)))
+ if (si.substring(start + j, start + j + 1)
+ .equals(sj.substring(start + j, start + j + 1)))
{
match++;
}
{
for (int j = 0; j < jlen; j++)
{
- if (si.substring(start + j, start + j + 1).equals(
- sj.substring(start + j, start + j + 1)))
+ if (si.substring(start + j, start + j + 1)
+ .equals(sj.substring(start + j, start + j + 1)))
{
match++;
}
* @deprecated use PIDModel.computePID()
*/
@Deprecated
- public final static float PID(String seq1, String seq2, int start, int end)
+ public final static float PID(String seq1, String seq2, int start,
+ int end)
{
return PID(seq1, seq2, start, end, true, false);
}
flattened.add(s);
}
}
- final SequenceI[] oneDArray = flattened.toArray(new SequenceI[flattened
- .size()]);
+ final SequenceI[] oneDArray = flattened
+ .toArray(new SequenceI[flattened.size()]);
return isNucleotide(oneDArray);
}
return false;
}
String coordsys = dasCoordinateSystemsLookup.get(string.toLowerCase());
- return coordsys == null ? false : coordsys.equals(dBRefEntry
- .getSource());
+ return coordsys == null ? false
+ : coordsys.equals(dBRefEntry.getSource());
}
/**
if (refa.getAccessionId() == null
|| refb.getAccessionId().equals(refa.getAccessionId()))
{
- if (refa.getMap() == null
- || (refb.getMap() != null && refb.getMap().equals(
- refa.getMap())))
+ if (refa.getMap() == null || (refb.getMap() != null
+ && refb.getMap().equals(refa.getMap())))
{
return true;
}
@Override
public boolean matches(DBRefEntry refa, DBRefEntry refb)
{
- if (refa.getSource() != null
- && refb.getSource() != null
+ if (refa.getSource() != null && refb.getSource() != null
&& DBRefUtils.getCanonicalName(refb.getSource()).equals(
DBRefUtils.getCanonicalName(refa.getSource())))
{
// We dont care about version
if (refa.getAccessionId() != null && refb.getAccessionId() != null
- // FIXME should be && not || here?
+ // FIXME should be && not || here?
|| refb.getAccessionId().equals(refa.getAccessionId()))
{
if ((refa.getMap() == null || refb.getMap() == null)
- || (refa.getMap() != null && refb.getMap() != null && refb
- .getMap().equals(refa.getMap())))
+ || (refa.getMap() != null && refb.getMap() != null
+ && refb.getMap().equals(refa.getMap())))
{
return true;
}
@Override
public boolean matches(DBRefEntry refa, DBRefEntry refb)
{
- if (refa.getSource() != null
- && refb.getSource() != null
+ if (refa.getSource() != null && refb.getSource() != null
&& DBRefUtils.getCanonicalName(refb.getSource()).equals(
DBRefUtils.getCanonicalName(refa.getSource())))
{
if ((refa.getMap() == null && refb.getMap() == null)
|| (refa.getMap() != null && refb.getMap() != null))
{
- if ((refb.getMap().getMap() == null && refa.getMap().getMap() == null)
+ if ((refb.getMap().getMap() == null
+ && refa.getMap().getMap() == null)
|| (refb.getMap().getMap() != null
- && refa.getMap().getMap() != null && refb
- .getMap().getMap().getInverse()
- .equals(refa.getMap().getMap())))
+ && refa.getMap().getMap() != null
+ && refb.getMap().getMap().getInverse()
+ .equals(refa.getMap().getMap())))
{
return true;
}
@Override
public boolean matches(DBRefEntry refa, DBRefEntry refb)
{
- if (refa.getSource() != null
- && refb.getSource() != null
+ if (refa.getSource() != null && refb.getSource() != null
&& DBRefUtils.getCanonicalName(refb.getSource()).equals(
DBRefUtils.getCanonicalName(refa.getSource())))
{
{
return true;
}
- if (refa.getMap() != null
- && refb.getMap() != null
- && ((refb.getMap().getMap() == null && refa.getMap()
- .getMap() == null) || (refb.getMap().getMap() != null
- && refa.getMap().getMap() != null && refb
- .getMap().getMap().equals(refa.getMap().getMap()))))
+ if (refa.getMap() != null && refb.getMap() != null
+ && ((refb.getMap().getMap() == null
+ && refa.getMap().getMap() == null)
+ || (refb.getMap().getMap() != null
+ && refa.getMap().getMap() != null
+ && refb.getMap().getMap()
+ .equals(refa.getMap().getMap()))))
{
return true;
}
@Override
public boolean matches(DBRefEntry refa, DBRefEntry refb)
{
- if (refa.getSource() != null
- && refb.getSource() != null
+ if (refa.getSource() != null && refb.getSource() != null
&& DBRefUtils.getCanonicalName(refb.getSource()).equals(
DBRefUtils.getCanonicalName(refa.getSource())))
{
return true;
}
if ((refa.getMap() != null && refb.getMap() != null)
- && (refb.getMap().getMap() == null && refa.getMap()
- .getMap() == null)
+ && (refb.getMap().getMap() == null
+ && refa.getMap().getMap() == null)
|| (refb.getMap().getMap() != null
- && refa.getMap().getMap() != null && (refb
- .getMap().getMap().equals(refa.getMap().getMap()))))
+ && refa.getMap().getMap() != null
+ && (refb.getMap().getMap()
+ .equals(refa.getMap().getMap()))))
{
return true;
}
{
return true;
}
- return DBRefUtils.getCanonicalName(o1).equals(
- DBRefUtils.getCanonicalName(o2));
+ return DBRefUtils.getCanonicalName(o1)
+ .equals(DBRefUtils.getCanonicalName(o2));
}
/**
public static DBRefEntry[] selectDbRefs(boolean selectDna,
DBRefEntry[] refs)
{
- return selectRefs(refs, selectDna ? DBRefSource.DNACODINGDBS
- : DBRefSource.PROTEINDBS);
+ return selectRefs(refs,
+ selectDna ? DBRefSource.DNACODINGDBS : DBRefSource.PROTEINDBS);
// could attempt to find other cross
// refs here - ie PDB xrefs
// (not dna, not protein seq)
}
// collate candidates and promote them
- DBRefEntry[] candidates = selectRefs(
- selfs.toArray(new DBRefEntry[0]),
+ DBRefEntry[] candidates = selectRefs(selfs.toArray(new DBRefEntry[0]),
promType.toArray(new String[0]));
if (candidates != null)
{
toPromote.add(cand);
if (!cand.isPrimaryCandidate())
{
- System.out.println("Warning: Couldn't promote dbref "
- + cand.toString() + " for sequence "
- + sequence.toString());
+ System.out.println(
+ "Warning: Couldn't promote dbref " + cand.toString()
+ + " for sequence " + sequence.toString());
}
}
}
{
w = width;
}
- else if (((fmt == 'd') || (fmt == 'i') || (fmt == 'x') || (fmt == 'X') || (fmt == 'o'))
- && (precision > 0))
+ else if (((fmt == 'd') || (fmt == 'i') || (fmt == 'x') || (fmt == 'X')
+ || (fmt == 'o')) && (precision > 0))
{
w = precision;
}
double factor = 1;
String leading_zeroes = "";
- for (int i = 1; (i <= precision) && (factor <= 0x7FFFFFFFFFFFFFFFL); i++)
+ for (int i = 1; (i <= precision)
+ && (factor <= 0x7FFFFFFFFFFFFFFFL); i++)
{
factor *= 10;
leading_zeroes = leading_zeroes + "0";
for (int pass = 0; pass < mtch.length; pass++)
{
int mlength = 3 + mtch[pass].length();
- if (link.indexOf("$" + mtch[pass] + "=/") == ptok[pass]
- && (p = link.indexOf("/=$", ptok[pass] + mlength)) > ptok[pass]
- + mlength)
+ if (link.indexOf("$" + mtch[pass] + "=/") == ptok[pass] && (p = link
+ .indexOf("/=$", ptok[pass] + mlength)) > ptok[pass] + mlength)
{
// Extract Regex and suffix
if (ptok[pass + 1] < p + 3)
regexReplace[pass] = link.substring(ptok[pass] + mlength, p);
try
{
- com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex.perlCode("/"
- + regexReplace[pass] + "/");
+ com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex
+ .perlCode("/" + regexReplace[pass] + "/");
if (rg == null)
{
invalidMessage = "Invalid Regular Expression : '"
* @param dsstring
* @return
*/
- private Hashtable replacementArgs(String[] idstrings,
- String[] seqstrings, String dsstring)
+ private Hashtable replacementArgs(String[] idstrings, String[] seqstrings,
+ String dsstring)
{
Hashtable rstrings = new Hashtable();
rstrings.put(tokens[0], idstrings);
rstrings.put(tokens[2], new String[] { dsstring });
if (idstrings.length != seqstrings.length)
{
- throw new Error(
- MessageManager
- .getString("error.idstring_seqstrings_only_one_per_sequence"));
+ throw new Error(MessageManager.getString(
+ "error.idstring_seqstrings_only_one_per_sequence"));
}
return rstrings;
}
* @return URL stub objects ready to pass to constructFrom
* @throws UrlStringTooLongException
*/
- public Object[] makeUrlStubs(String[] ids, String[] seqstr,
- String string, boolean b) throws UrlStringTooLongException
+ public Object[] makeUrlStubs(String[] ids, String[] seqstr, String string,
+ boolean b) throws UrlStringTooLongException
{
Hashtable rstrings = replacementArgs(ids, seqstr, string);
Object[] stubs = makeUrlsIf(false, rstrings, b);
if (stubs != null)
{
return new Object[] { stubs[0], stubs[1], rstrings,
- new boolean[] { b } };
+ new boolean[]
+ { b } };
}
// TODO Auto-generated method stub
return null;
* }, String[] { url })}
* @throws UrlStringTooLongException
*/
- protected Object[] makeUrlsIf(boolean createFullUrl,
- Hashtable repstrings, boolean onlyIfMatches)
- throws UrlStringTooLongException
+ protected Object[] makeUrlsIf(boolean createFullUrl, Hashtable repstrings,
+ boolean onlyIfMatches) throws UrlStringTooLongException
{
int pass = 0;
{
throw new Error(MessageManager.formatMessage(
"error.cannot_have_mixed_length_replacement_vectors",
- new String[] { (mtch[i]),
+ new String[]
+ { (mtch[i]),
Integer.valueOf(idseq[i].length).toString(),
Integer.valueOf(maxs).toString() }));
}
}
else
{
- throw new Error(
- MessageManager
- .getString("error.cannot_have_zero_length_vector_replacement_strings"));
+ throw new Error(MessageManager.getString(
+ "error.cannot_have_zero_length_vector_replacement_strings"));
}
}
// iterate through input, collating segments to be inserted into url
matched[pass] = new StringBuffer();
if (regexReplace[pass] != null)
{
- rgxs[pass] = com.stevesoft.pat.Regex.perlCode("/"
- + regexReplace[pass] + "/");
+ rgxs[pass] = com.stevesoft.pat.Regex
+ .perlCode("/" + regexReplace[pass] + "/");
}
else
{
}
return new Object[] { new int[] { seqsmatched }, thismatched, matched,
- new String[] { submiturl.toString() } };
+ new String[]
+ { submiturl.toString() } };
}
/**
"EnVision2|Seqs|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=$SEQUENCEIDS$&datasetName=$DATASETID$&input=$SEQUENCES$&inputType=1|,",
"EnVision2 Seqs|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([a-zA-Z]+)/=$&inputType=1|,",
"EnVision2 Seqs|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/[A-Za-z]+/=$&inputType=1|,"
- /*
- * http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?input=P38389,P38398
- * &inputType=0&workflow=Enfin%20Default%20Workflow&datasetName=
- * linkInDatasetFromPRIDE
- */
+ /*
+ * http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?input=P38389,P38398
+ * &inputType=0&workflow=Enfin%20Default%20Workflow&datasetName=
+ * linkInDatasetFromPRIDE
+ */
};
- SequenceI[] seqs = new SequenceI[] { new Sequence(
- "StupidLabel:gi|9234|pdb|102L|A",
- "asdiasdpasdpadpwpadasdpaspdw"), };
+ SequenceI[] seqs = new SequenceI[] {
+ new Sequence("StupidLabel:gi|9234|pdb|102L|A",
+ "asdiasdpasdpadpwpadasdpaspdw"), };
String[][] seqsandids = formStrings(seqs);
for (int i = 0; i < links.length; i++)
{
if (ul.isValid())
{
System.out.println("\n\n\n");
- System.out.println("Link " + i + " " + links[i] + " : "
- + ul.toString());
+ System.out.println(
+ "Link " + i + " " + links[i] + " : " + ul.toString());
System.out.println(" pref : " + ul.getUrl_prefix());
System.out.println(" IdReplace : " + ul.getIDRegexReplace());
System.out.println(" SeqReplace : " + ul.getSeqRegexReplace());
System.out.println(" Suffixes : " + ul.getUrl_suffix());
- System.out
- .println("<insert input id and sequence strings here> Without onlyIfMatches:");
+ System.out.println(
+ "<insert input id and sequence strings here> Without onlyIfMatches:");
Object[] urls;
try
{
{
System.out.println("too long exception " + ex);
}
- System.out
- .println("<insert input id and sequence strings here> With onlyIfMatches set:");
+ System.out.println(
+ "<insert input id and sequence strings here> With onlyIfMatches set:");
try
{
urls = ul.makeUrls(seqsandids[0], seqsandids[1], "mydataset",
public enum TYPE
{
EPS("EPS", MessageManager.getString("label.eps_file"), getEPSChooser()),
- PNG("PNG", MessageManager.getString("label.png_image"), getPNGChooser()),
+ PNG("PNG", MessageManager.getString("label.png_image"),
+ getPNGChooser()),
SVG("SVG", "SVG", getSVGChooser());
private JalviewFileChooser chooser;
if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
{
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
- .getSelectedFile().getParent());
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+ chooser.getSelectedFile().getParent());
file = chooser.getSelectedFile();
}
else
{
System.out.println("Error creating " + type.getName() + " file.");
- setProgressMessage(MessageManager.formatMessage(
- "info.error_creating_file", type.getName()));
+ setProgressMessage(MessageManager
+ .formatMessage("info.error_creating_file", type.getName()));
}
}
}
pg.setAccurateTextMode(accurateText);
graphics = pg;
- setProgressMessage(MessageManager.formatMessage(
- "status.export_complete", type.getName()));
+ setProgressMessage(MessageManager
+ .formatMessage("status.export_complete", type.getName()));
} catch (Exception ex)
{
}
Graphics2D ig2 = (Graphics2D) graphics;
ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
RenderingHints.VALUE_ANTIALIAS_ON);
- setProgressMessage(MessageManager.formatMessage(
- "status.export_complete", type.getName()));
+ setProgressMessage(MessageManager
+ .formatMessage("status.export_complete", type.getName()));
}
SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
}
- setProgressMessage(MessageManager.formatMessage(
- "status.export_complete", type.getName()));
+ setProgressMessage(MessageManager
+ .formatMessage("status.export_complete", type.getName()));
graphics = g2;
}
{
return false;
}
- return Arrays
- .deepEquals(fromShifts.toArray(), obj.fromShifts.toArray())
- && Arrays
- .deepEquals(toShifts.toArray(), obj.toShifts.toArray());
+ return Arrays.deepEquals(fromShifts.toArray(), obj.fromShifts.toArray())
+ && Arrays.deepEquals(toShifts.toArray(),
+ obj.toShifts.toArray());
}
/**
* drop this range if it lies within the last range
*/
if ((lastDirection == 1 && range[0] >= lastRange[0]
- && range[0] <= lastRange[1] && range[1] >= lastRange[0] && range[1] <= lastRange[1])
+ && range[0] <= lastRange[1] && range[1] >= lastRange[0]
+ && range[1] <= lastRange[1])
|| (lastDirection == -1 && range[0] <= lastRange[0]
&& range[0] >= lastRange[1]
- && range[1] <= lastRange[0] && range[1] >= lastRange[1]))
+ && range[1] <= lastRange[0]
+ && range[1] >= lastRange[1]))
{
changed = true;
continue;
boolean sameDirection = range[1] == range[0]
|| direction == lastDirection;
boolean extending = range[0] == lastRange[1] + lastDirection;
- boolean overlapping = (lastDirection == 1 && range[0] >= lastRange[0] && range[0] <= lastRange[1])
- || (lastDirection == -1 && range[0] <= lastRange[0] && range[0] >= lastRange[1]);
+ boolean overlapping = (lastDirection == 1 && range[0] >= lastRange[0]
+ && range[0] <= lastRange[1])
+ || (lastDirection == -1 && range[0] <= lastRange[0]
+ && range[0] >= lastRange[1]);
if (sameDirection && (overlapping || extending))
{
lastRange[1] = range[1];
// TODO not used - remove?
if (local)
{
- return ((getFromLowest() >= map.getFromLowest() && getFromHighest() <= map
- .getFromHighest()) || (getFromLowest() <= map.getFromLowest() && getFromHighest() >= map
- .getFromHighest()));
+ return ((getFromLowest() >= map.getFromLowest()
+ && getFromHighest() <= map.getFromHighest())
+ || (getFromLowest() <= map.getFromLowest()
+ && getFromHighest() >= map.getFromHighest()));
}
else
{
- return ((getToLowest() >= map.getToLowest() && getToHighest() <= map
- .getToHighest()) || (getToLowest() <= map.getToLowest() && getToHighest() >= map
- .getToHighest()));
+ return ((getToLowest() >= map.getToLowest()
+ && getToHighest() <= map.getToHighest())
+ || (getToLowest() <= map.getToLowest()
+ && getToHighest() >= map.getToHighest()));
}
}
* Shift Delete start position left, as it acts on positions to its
* right.
*/
- int mappedEditPos = action == Action.DELETE_GAP ? match[0]
- - mappedCount : match[0];
+ int mappedEditPos = action == Action.DELETE_GAP
+ ? match[0] - mappedCount
+ : match[0];
Edit e = result.new Edit(action, new SequenceI[] { targetSeq },
mappedEditPos, mappedCount, gapChar);
result.addEdit(e);
*/
if (action == Action.INSERT_GAP)
{
- copyTarget.setSequence(new String(StringUtils.insertCharAt(
- copyTarget.getSequence(), mappedEditPos, mappedCount,
- gapChar)));
+ copyTarget.setSequence(new String(
+ StringUtils.insertCharAt(copyTarget.getSequence(),
+ mappedEditPos, mappedCount, gapChar)));
}
else if (action == Action.DELETE_GAP)
{
- copyTarget.setSequence(new String(StringUtils.deleteChars(
- copyTarget.getSequence(), mappedEditPos,
- mappedEditPos + mappedCount)));
+ copyTarget.setSequence(new String(
+ StringUtils.deleteChars(copyTarget.getSequence(),
+ mappedEditPos, mappedEditPos + mappedCount)));
}
}
}
for (AlignedCodonFrame acf : codonFrames)
{
- SequenceI mappedSequence = targetIsNucleotide ? acf
- .getDnaForAaSeq(selected) : acf.getAaForDnaSeq(selected);
+ SequenceI mappedSequence = targetIsNucleotide
+ ? acf.getDnaForAaSeq(selected)
+ : acf.getAaForDnaSeq(selected);
if (mappedSequence != null)
{
for (SequenceI seq : mapTo.getAlignment().getSequences())
* Found a sequence mapping. Locate the start/end mapped residues.
*/
List<AlignedCodonFrame> mapping = Arrays
- .asList(new AlignedCodonFrame[] { acf });
+ .asList(new AlignedCodonFrame[]
+ { acf });
SearchResultsI sr = buildSearchResults(selected,
startResiduePos, mapping);
for (SearchResultMatchI m : sr.getResults())
* returns a base 1 position, SequenceGroup uses base 0
*/
int mappedStartCol = seq.findIndex(mappedStartResidue) - 1;
- minStartCol = minStartCol == -1 ? mappedStartCol : Math.min(
- minStartCol, mappedStartCol);
+ minStartCol = minStartCol == -1 ? mappedStartCol
+ : Math.min(minStartCol, mappedStartCol);
int mappedEndCol = seq.findIndex(mappedEndResidue) - 1;
- maxEndCol = maxEndCol == -1 ? mappedEndCol : Math.max(
- maxEndCol, mappedEndCol);
+ maxEndCol = maxEndCol == -1 ? mappedEndCol
+ : Math.max(maxEndCol, mappedEndCol);
mappedGroup.addSequence(seq, false);
break;
}
* the mappings available
* @return
*/
- public static CommandI mapOrderCommand(OrderCommand command,
- boolean undo, AlignmentI mapTo, List<AlignedCodonFrame> mappings)
+ public static CommandI mapOrderCommand(OrderCommand command, boolean undo,
+ AlignmentI mapTo, List<AlignedCodonFrame> mappings)
{
SequenceI[] sortOrder = command.getSequenceOrder(undo);
List<SequenceI> mappedOrder = new ArrayList<>();
* @param toSequences
* @param fromGapChar
*/
- protected static void mapColumn(int col,
- List<AlignedCodonFrame> mappings, ColumnSelection mappedColumns,
- List<SequenceI> fromSequences, List<SequenceI> toSequences,
- char fromGapChar)
+ protected static void mapColumn(int col, List<AlignedCodonFrame> mappings,
+ ColumnSelection mappedColumns, List<SequenceI> fromSequences,
+ List<SequenceI> toSequences, char fromGapChar)
{
int[] mappedTo = findMappedColumns(col, mappings, fromSequences,
toSequences, fromGapChar);
{
if (mapping.involvesSequence(seq))
{
- List<char[]> codons = mapping.getMappedCodons(
- seq.getDatasetSequence(), dsPos);
+ List<char[]> codons = mapping
+ .getMappedCodons(seq.getDatasetSequence(), dsPos);
if (codons != null)
{
result.addAll(codons);
SequenceI otherDataset = otherseq.getDatasetSequence();
if (otherseq == sequence
|| otherseq == sequence.getDatasetSequence()
- || (otherDataset != null && (otherDataset == sequence || otherDataset == sequence
- .getDatasetSequence())))
+ || (otherDataset != null && (otherDataset == sequence
+ || otherDataset == sequence
+ .getDatasetSequence())))
{
// skip sequences in subset which directly relate to sequence
continue;
{
if (range.length % 2 != 0)
{
- System.err.println("Error unbalance start/end ranges: "
- + ranges.toString());
+ System.err.println(
+ "Error unbalance start/end ranges: " + ranges.toString());
return 0;
}
for (int i = 0; i < range.length - 1; i += 2)
private static ResourceBundle rb;
- private static Logger log = Logger.getLogger(MessageManager.class
- .getCanonicalName());
+ private static Logger log = Logger
+ .getLogger(MessageManager.class.getCanonicalName());
private static Locale loc;
name = rb.getString(smkey);
} catch (Exception x)
{
- log.finest("I18N missing key with root " + keyroot + ": " + loc
- + "\t" + smkey);
+ log.finest("I18N missing key with root " + keyroot + ": " + loc + "\t"
+ + smkey);
}
return name;
}
{
// instead of parsing the html into plaintext
// clean the description ready for embedding in html
- sb = new StringBuilder(LEFT_ANGLE_BRACKET_PATTERN
- .matcher(description).replaceAll("<"));
+ sb = new StringBuilder(LEFT_ANGLE_BRACKET_PATTERN.matcher(description)
+ .replaceAll("<"));
}
content = translateEntities(sb.toString());
}
{
return false;
}
- return (Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() & e
- .getModifiers()) != 0;
+ return (Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+ & e.getModifiers()) != 0;
// could we use e.isMetaDown() here?
}
return e.isControlDown();
@Override
public int compare(Integer o1, Integer o2)
{
- return ascending ? Float.compare(values[o1], values[o2]) : Float
- .compare(values[o2], values[o1]);
+ return ascending ? Float.compare(values[o1], values[o2])
+ : Float.compare(values[o2], values[o1]);
}
}
@Override
public int compare(Integer o1, Integer o2)
{
- return ascending ? Integer.compare(values[o1], values[o2]) : Integer
- .compare(values[o2], values[o1]);
+ return ascending ? Integer.compare(values[o1], values[o2])
+ : Integer.compare(values[o2], values[o1]);
}
}
@Override
public int compare(Integer o1, Integer o2)
{
- return ascending ? values[o1].compareTo(values[o2]) : values[o2]
- .compareTo(values[o1]);
+ return ascending ? values[o1].compareTo(values[o2])
+ : values[o2].compareTo(values[o1]);
}
}
/*
* Copy sorted positive values after the negatives and zeros
*/
- System.arraycopy(nonZeroFloats, negativeCount, arr, negativeCount
- + zerosCount, positiveCount);
- System.arraycopy(nonZeroChars, negativeCount, s, negativeCount
- + zerosCount, positiveCount);
+ System.arraycopy(nonZeroFloats, negativeCount, arr,
+ negativeCount + zerosCount, positiveCount);
+ System.arraycopy(nonZeroChars, negativeCount, s,
+ negativeCount + zerosCount, positiveCount);
}
/**
/*
* Copy sorted positive values after the negatives and zeros
*/
- System.arraycopy(nonZeroInts, negativeCount, arr, negativeCount
- + zerosCount, positiveCount);
- System.arraycopy(nonZeroChars, negativeCount, s, negativeCount
- + zerosCount, positiveCount);
+ System.arraycopy(nonZeroInts, negativeCount, arr,
+ negativeCount + zerosCount, positiveCount);
+ System.arraycopy(nonZeroChars, negativeCount, s,
+ negativeCount + zerosCount, positiveCount);
}
/**
}
else
{
- try {
+ try
+ {
newValue = shortProfile.add(key, value);
- } catch (ArithmeticException e) {
+ } catch (ArithmeticException e)
+ {
handleOverflow();
newValue = intProfile.add(key, value);
}
* @param delimiter
* @return elements separated by separator
*/
- public static String[] separatorListToArray(String input, String delimiter)
+ public static String[] separatorListToArray(String input,
+ String delimiter)
{
int seplen = delimiter.length();
if (input == null || input.equals("") || input.equals(delimiter))
if (wasescaped || wasquoted)
{
// append to previous pos
- jv.set(jv.size() - 1,
- lstitem = lstitem + delimiter
- + input.substring(cp, pos + escape));
+ jv.set(jv.size() - 1, lstitem = lstitem + delimiter
+ + input.substring(cp, pos + escape));
}
else
{
}
if (DEBUG)
{
- System.err.println("Empty Array from '" + delimiter
- + "' separated List");
+ System.err.println(
+ "Empty Array from '" + delimiter + "' separated List");
}
return null;
}
}
if (DEBUG)
{
- System.err.println("Returning '" + separator
- + "' separated List:\n");
+ System.err
+ .println("Returning '" + separator + "' separated List:\n");
System.err.println(v);
}
return v.toString();
}
if (DEBUG)
{
- System.err.println("Returning empty '" + separator
- + "' separated List\n");
+ System.err.println(
+ "Returning empty '" + separator + "' separated List\n");
}
return "" + separator;
}
}
} catch (NumberFormatException e)
{
- System.err.println("Invalid version format found: "
- + e.getMessage());
+ System.err
+ .println("Invalid version format found: " + e.getMessage());
return 0;
}
}
.getDefaultRenderer();
if (defaultRenderer instanceof SortableHeaderRenderer)
{
- this.tableHeader
- .setDefaultRenderer(((SortableHeaderRenderer) defaultRenderer).tableCellRenderer);
+ this.tableHeader.setDefaultRenderer(
+ ((SortableHeaderRenderer) defaultRenderer).tableCellRenderer);
}
}
this.tableHeader = tableHeader;
JLabel l = (JLabel) c;
l.setHorizontalTextPosition(JLabel.LEFT);
int modelColumn = table.convertColumnIndexToModel(column);
- l.setIcon(getHeaderRendererIcon(modelColumn, l.getFont().getSize()));
+ l.setIcon(
+ getHeaderRendererIcon(modelColumn, l.getFont().getSize()));
}
return c;
}
String var = (usesDBaccession ? DB_ACCESSION : SEQUENCE_ID);
return urlPrefix
- + (dynamic ? (DELIM + var + ((regexReplace != null) ? EQUALS
- + regexReplace + EQUALS + DELIM : DELIM)) : "")
+ + (dynamic
+ ? (DELIM + var
+ + ((regexReplace != null)
+ ? EQUALS + regexReplace + EQUALS + DELIM
+ : DELIM))
+ : "")
+ ((urlSuffix == null) ? "" : urlSuffix);
}
{
if (regexReplace != null)
{
- com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex.perlCode("/"
- + regexReplace + "/");
+ com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex
+ .perlCode("/" + regexReplace + "/");
if (rg.search(idstring))
{
int ns = rg.numSubs();
if (rg.matchedFrom(s) > -1)
{
subs.addElement(rg.stringMatched(s));
- subs.addElement(urlPrefix + rg.stringMatched(s)
- + urlSuffix);
+ subs.addElement(
+ urlPrefix + rg.stringMatched(s) + urlSuffix);
}
s++;
}
regexReplace = link.substring(sqidPos + startLength, p);
try
{
- com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex.perlCode("/"
- + regexReplace + "/");
+ com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex
+ .perlCode("/" + regexReplace + "/");
if (rg == null)
{
invalidMessage = "Invalid Regular Expression : '" + regexReplace
{
// collect matching db-refs
DBRefEntry[] dbr = DBRefUtils.selectRefs(seq.getDBRefs(),
- new String[] { target });
+ new String[]
+ { target });
// if there are any dbrefs which match up with the link
if (dbr != null)
* @author jimp
*
*/
-public abstract class AlignmentViewport implements AlignViewportI,
- CommandListener, VamsasSource
+public abstract class AlignmentViewport
+ implements AlignViewportI, CommandListener, VamsasSource
{
final protected ViewportRanges ranges;
viewStyle.setSeqNameItalics(default1);
}
-
-
@Override
public AlignmentI getAlignment()
{
sg.setColourScheme(cs);
if (cs != null)
{
- sg.getGroupColourScheme()
- .alignmentChanged(sg, hiddenRepSequences);
+ sg.getGroupColourScheme().alignmentChanged(sg,
+ hiddenRepSequences);
}
}
}
@Override
public ColourSchemeI getGlobalColourScheme()
{
- return residueShading == null ? null : residueShading
- .getColourScheme();
+ return residueShading == null ? null : residueShading.getColourScheme();
}
@Override
{
return;
}
- if (calculator
- .getRegisteredWorkersOfClass(jalview.workers.ConservationThread.class) == null)
+ if (calculator.getRegisteredWorkersOfClass(
+ jalview.workers.ConservationThread.class) == null)
{
- calculator.registerWorker(new jalview.workers.ConservationThread(
- this, ap));
+ calculator.registerWorker(
+ new jalview.workers.ConservationThread(this, ap));
}
}
{
return;
}
- if (calculator.getRegisteredWorkersOfClass(ConsensusThread.class) == null)
+ if (calculator
+ .getRegisteredWorkersOfClass(ConsensusThread.class) == null)
{
calculator.registerWorker(new ConsensusThread(this, ap));
}
}
if (doConsensus)
{
- if (calculator
- .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null)
+ if (calculator.getRegisteredWorkersOfClass(
+ ComplementConsensusThread.class) == null)
{
calculator
.registerWorker(new ComplementConsensusThread(this, ap));
{
return;
}
- if (calculator.getRegisteredWorkersOfClass(StrucConsensusThread.class) == null)
+ if (calculator.getRegisteredWorkersOfClass(
+ StrucConsensusThread.class) == null)
{
calculator.registerWorker(new StrucConsensusThread(this, ap));
}
{
if (sequenceSetID != null)
{
- System.err
- .println("Warning - overwriting a sequenceSetId for a viewport!");
+ System.err.println(
+ "Warning - overwriting a sequenceSetId for a viewport!");
}
sequenceSetID = new String(newid);
}
selectionGroup = new SequenceGroup();
selectionGroup.setEndRes(alignment.getWidth() - 1);
}
- List<SequenceI> tmp = alignment.getHiddenSequences().showAll(
- hiddenRepSequences);
+ List<SequenceI> tmp = alignment.getHiddenSequences()
+ .showAll(hiddenRepSequences);
for (SequenceI seq : tmp)
{
selectionGroup.addSequence(seq, false);
int startSeq = ranges.getStartSeq();
int endSeq = ranges.getEndSeq();
- List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(
- index, hiddenRepSequences);
+ List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(index,
+ hiddenRepSequences);
if (tmp.size() > 0)
{
if (selectionGroup == null)
}
int gsize = selectionGroup.getSize();
- SequenceI[] hseqs = selectionGroup.getSequences().toArray(
- new SequenceI[gsize]);
+ SequenceI[] hseqs = selectionGroup.getSequences()
+ .toArray(new SequenceI[gsize]);
hideSequence(hseqs);
setSelectionGroup(null);
*/
public boolean isHiddenRepSequence(SequenceI seq)
{
- return (hiddenRepSequences != null && hiddenRepSequences
- .containsKey(seq));
+ return (hiddenRepSequences != null
+ && hiddenRepSequences.containsKey(seq));
}
/**
@Override
public int adjustForHiddenSeqs(int alignmentIndex)
{
- return alignment.getHiddenSequences().adjustForHiddenSeqs(
- alignmentIndex);
+ return alignment.getHiddenSequences()
+ .adjustForHiddenSeqs(alignmentIndex);
}
@Override
boolean selectedOnly, boolean markGroups)
{
return new AlignmentView(alignment, alignment.getHiddenColumns(),
- selectionGroup, alignment.getHiddenColumns() != null
+ selectionGroup,
+ alignment.getHiddenColumns() != null
&& alignment.getHiddenColumns().hasHiddenColumns(),
- selectedOnly,
- markGroups);
+ selectedOnly, markGroups);
}
@Override
if (alignment.getHiddenColumns() != null
&& alignment.getHiddenColumns().hasHiddenColumns())
{
- selection = alignment.getHiddenColumns().getVisibleSequenceStrings(
- start, end, seqs);
+ selection = alignment.getHiddenColumns()
+ .getVisibleSequenceStrings(start, end, seqs);
}
else
{
if (selectedOnly && selectionGroup != null)
{
alignment.getHiddenColumns().makeVisibleAnnotation(
- selectionGroup.getStartRes(),
- selectionGroup.getEndRes(), clone);
+ selectionGroup.getStartRes(), selectionGroup.getEndRes(),
+ clone);
}
else
{
{
gapcounts = new AlignmentAnnotation("Occupancy",
MessageManager.getString("label.occupancy_descr"),
- new Annotation[1], 0f,
- alignment.getHeight(), AlignmentAnnotation.BAR_GRAPH);
+ new Annotation[1], 0f, alignment.getHeight(),
+ AlignmentAnnotation.BAR_GRAPH);
gapcounts.hasText = true;
gapcounts.autoCalculated = true;
gapcounts.scaleColLabel = true;
{
conservation = new AlignmentAnnotation("Conservation",
MessageManager.formatMessage("label.conservation_descr",
- getConsPercGaps()), new Annotation[1],
- 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
+ getConsPercGaps()),
+ new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
conservation.hasText = true;
conservation.autoCalculated = true;
alignment.addAnnotation(conservation);
viewStyle = new ViewStyle(settingsForView);
if (residueShading != null)
{
- residueShading.setConservationApplied(settingsForView
- .isConservationColourSelected());
+ residueShading.setConservationApplied(
+ settingsForView.isConservationColourSelected());
}
}
return sortAnnotationsBy;
}
- public void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy)
+ public void setSortAnnotationsBy(
+ SequenceAnnotationOrder sortAnnotationsBy)
{
this.sortAnnotationsBy = sortAnnotationsBy;
}
return 0;
}
boolean iAmProtein = !getAlignment().isNucleotide();
- AlignmentI proteinAlignment = iAmProtein ? getAlignment() : complement
- .getAlignment();
+ AlignmentI proteinAlignment = iAmProtein ? getAlignment()
+ : complement.getAlignment();
if (proteinAlignment == null)
{
return 0;
*/
int lastSeq = alignment.getHeight() - 1;
List<AlignedCodonFrame> seqMappings = null;
- for (int seqNo = ranges.getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
+ for (int seqNo = ranges
+ .getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
{
sequence = getAlignment().getSequenceAt(seqNo);
if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
{
continue;
}
- seqMappings = MappingUtils
- .findMappingsForSequenceAndOthers(sequence, mappings,
- getCodingComplement().getAlignment().getSequences());
+ seqMappings = MappingUtils.findMappingsForSequenceAndOthers(sequence,
+ mappings,
+ getCodingComplement().getAlignment().getSequences());
if (!seqMappings.isEmpty())
{
break;
}
}
}
-
+
SequenceI sq = new Sequence("Consensus", seqs.toString());
sq.setDescription("Percentage Identity Consensus "
+ ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
/*
* Given the centre x position, calculate the box's left x position
*/
- protected abstract int getLeftXFromCentreX(int mousex, HiddenColumns hidden);
+ protected abstract int getLeftXFromCentreX(int mousex,
+ HiddenColumns hidden);
/*
* Given the centre y position, calculate the box's top y position
int visYAsRes = hiddenSeqs.findIndexWithoutHiddenSeqs(vpy) + ydiff;
// update viewport accordingly
- updateViewportFromTopLeft(visXAsRes, visYAsRes,
- hiddenSeqs,
- hiddenCols);
+ updateViewportFromTopLeft(visXAsRes, visYAsRes, hiddenSeqs, hiddenCols);
}
@Override
// went past the end of the alignment, adjust backwards
if (ranges.getEndSeq() < visAlignHeight)
{
- visYAsSeq = hiddenSeqs.findIndexWithoutHiddenSeqs(hiddenSeqs
- .subtractVisibleRows(vpheight - 1, alheight - 1));
+ visYAsSeq = hiddenSeqs.findIndexWithoutHiddenSeqs(
+ hiddenSeqs.subtractVisibleRows(vpheight - 1, alheight - 1));
}
else
{
int startSeq = hiddenSeqs.adjustForHiddenSeqs(ranges.getStartSeq());
int endSeq = hiddenSeqs.adjustForHiddenSeqs(ranges.getEndSeq());
- setBoxPosition(startRes, startSeq, endRes - startRes + 1, endSeq
- - startSeq + 1);
+ setBoxPosition(startRes, startSeq, endRes - startRes + 1,
+ endSeq - startSeq + 1);
}
@Override
public AlignmentColsCollectionI getColumns(AlignmentI al)
{
- return new AllColsCollection(0,
- ranges.getAbsoluteAlignmentWidth() - 1, al);
+ return new AllColsCollection(0, ranges.getAbsoluteAlignmentWidth() - 1,
+ al);
}
@Override
public AlignmentRowsCollectionI getRows(AlignmentI al)
{
- return new AllRowsCollection(0,
- ranges.getAbsoluteAlignmentHeight() - 1,
+ return new AllRowsCollection(0, ranges.getAbsoluteAlignmentHeight() - 1,
al);
}
* @param params
*/
public PCAModel(AlignmentView seqData, SequenceI[] sqs, boolean nuc,
- ScoreModelI modelName,
- SimilarityParamsI params)
+ ScoreModelI modelName, SimilarityParamsI params)
{
seqstrings = seqData;
seqs = sqs;
}
}
}
-
+
/**
* Adjust sequence position for page up. Fires a property change event.
*/
getViewportHeight());
}
}
-
+
/**
* Adjust sequence position for page down. Fires a property change event.
*/
return regexSearchFields;
}
- public void addRegexSearchField(SearchableAnnotationField regexSearchField)
+ public void addRegexSearchField(
+ SearchableAnnotationField regexSearchField)
{
this.regexSearchFields.add(regexSearchField);
}
import java.util.Set;
import java.util.concurrent.ConcurrentHashMap;
-public abstract class FeatureRendererModel implements
- jalview.api.FeatureRenderer
+public abstract class FeatureRendererModel
+ implements jalview.api.FeatureRenderer
{
/**
if (r[0] != 0 || mm[0] < 0.0)
{
r[0] = 1;
- r[1] = (byte) ((int) 128.0 + 127.0 * (sequenceFeature.score / mm[1]));
+ r[1] = (byte) ((int) 128.0
+ + 127.0 * (sequenceFeature.score / mm[1]));
}
else
{
}
@Override
- public List<SequenceFeature> findFeaturesAtRes(SequenceI sequence, int res)
+ public List<SequenceFeature> findFeaturesAtRes(SequenceI sequence,
+ int res)
{
ArrayList<SequenceFeature> tmp = new ArrayList<SequenceFeature>();
SequenceFeature[] features = sequence.getSequenceFeatures();
{
for (int i = 0; i < features.length; i++)
{
- if (!av.areFeaturesDisplayed()
- || !av.getFeaturesDisplayed().isVisible(
- features[i].getType()))
+ if (!av.areFeaturesDisplayed() || !av.getFeaturesDisplayed()
+ .isVisible(features[i].getType()))
{
continue;
}
- if (features[i].featureGroup != null
- && featureGroups != null
+ if (features[i].featureGroup != null && featureGroups != null
&& featureGroups.containsKey(features[i].featureGroup)
&& !featureGroups.get(features[i].featureGroup)
.booleanValue())
// lies between start and end
if ((features[i].getBegin() == res || features[i].getEnd() == res)
|| (!features[i].isContactFeature()
- && (features[i].getBegin() < res) && (features[i]
- .getEnd() >= res)))
+ && (features[i].getBegin() < res)
+ && (features[i].getEnd() >= res)))
{
tmp.add(features[i]);
}
{
if (initOrders)
{
- setOrder(oldRender[j], (1 - (1 + (float) j) / oldRender.length));
+ setOrder(oldRender[j],
+ (1 - (1 + (float) j) / oldRender.length));
}
if (allfeatures.contains(oldRender[j]))
{
}
else
{
- av.setFeaturesDisplayed(av_featuresdisplayed = new FeaturesDisplayed());
+ av.setFeaturesDisplayed(
+ av_featuresdisplayed = new FeaturesDisplayed());
}
}
else
{
// conflict between applet and desktop - featureGroups returns the map in
// the desktop featureRenderer
- return (featureGroups == null) ? Arrays.asList(new String[0]) : Arrays
- .asList(featureGroups.keySet().toArray(new String[0]));
+ return (featureGroups == null) ? Arrays.asList(new String[0])
+ : Arrays.asList(featureGroups.keySet().toArray(new String[0]));
}
- public boolean checkGroupVisibility(String group, boolean newGroupsVisible)
+ public boolean checkGroupVisibility(String group,
+ boolean newGroupsVisible)
{
if (featureGroups == null)
{
&& getThreshold() == vs.getThreshold()
&& getThresholdTextColour() == vs.getThresholdTextColour()
&& isUpperCasebold() == vs.isUpperCasebold()
- && getWrapAlignment() == vs.getWrapAlignment() && getWrappedWidth() == vs
- .getWrappedWidth());
+ && getWrapAlignment() == vs.getWrapAlignment()
+ && getWrappedWidth() == vs.getWrappedWidth());
/*
* and compare non-primitive types; syntax below will match null with null
* values
*/
- match = match
- && String.valueOf(getFontName()).equals(
- String.valueOf(vs.getFontName()));
- match = match
- && String.valueOf(getTextColour()).equals(
- String.valueOf(vs.getTextColour()));
- match = match
- && String.valueOf(getTextColour2()).equals(
- String.valueOf(vs.getTextColour2()));
+ match = match && String.valueOf(getFontName())
+ .equals(String.valueOf(vs.getFontName()));
+ match = match && String.valueOf(getTextColour())
+ .equals(String.valueOf(vs.getTextColour()));
+ match = match && String.valueOf(getTextColour2())
+ .equals(String.valueOf(vs.getTextColour2()));
return match;
// return equivalent(this, (ViewStyle) other);
}
{
restartable = Collections
.synchronizedList(new ArrayList<AlignCalcWorkerI>());
- blackList = Collections
- .synchronizedList(new ArrayList<Class<? extends AlignCalcWorkerI>>());
+ blackList = Collections.synchronizedList(
+ new ArrayList<Class<? extends AlignCalcWorkerI>>());
inProgress = Collections
.synchronizedList(new ArrayList<AlignCalcWorkerI>());
- updating = Collections
- .synchronizedMap(new Hashtable<Class<? extends AlignCalcWorkerI>, List<AlignCalcWorkerI>>());
+ updating = Collections.synchronizedMap(
+ new Hashtable<Class<? extends AlignCalcWorkerI>, List<AlignCalcWorkerI>>());
canUpdate = new HashSet<AlignCalcWorkerI>();
}
List<AlignCalcWorkerI> upd = updating.get(worker.getClass());
if (upd == null)
{
- updating.put(
- worker.getClass(),
- upd = Collections
- .synchronizedList(new ArrayList<AlignCalcWorkerI>()));
+ updating.put(worker.getClass(), upd = Collections
+ .synchronizedList(new ArrayList<AlignCalcWorkerI>()));
}
synchronized (upd)
{
}
@Override
- public boolean workingInvolvedWith(AlignmentAnnotation alignmentAnnotation)
+ public boolean workingInvolvedWith(
+ AlignmentAnnotation alignmentAnnotation)
{
synchronized (inProgress)
{
/**
* Factory class with methods which allow clients (including external scripts
- * such as Groovy) to 'register and forget' an alignment annotation calculator. <br>
+ * such as Groovy) to 'register and forget' an alignment annotation calculator.
+ * <br>
* Currently supports two flavours of calculator:
* <ul>
* <li>a simple 'feature counter' which counts any desired score derivable from
- * residue value and any sequence features at each position of the alignment</li>
+ * residue value and any sequence features at each position of the
+ * alignment</li>
* <li>a 'general purpose' calculator which computes one or more complete
* AlignmentAnnotation objects</li>
* </ul>
*/
public static void newCalculator(FeatureSetCounterI counter)
{
- AlignmentViewPanel currentAlignFrame = Jalview.getCurrentAlignFrame().alignPanel;
+ AlignmentViewPanel currentAlignFrame = Jalview
+ .getCurrentAlignFrame().alignPanel;
if (currentAlignFrame == null)
{
- System.err
- .println("Can't register calculator as no alignment window has focus");
+ System.err.println(
+ "Can't register calculator as no alignment window has focus");
return;
}
new ColumnCounterSetWorker(currentAlignFrame.getAlignViewport(),
}
else
{
- System.err
- .println("Can't register calculator as no alignment window has focus");
+ System.err.println(
+ "Can't register calculator as no alignment window has focus");
}
}
public static Annotation newAnnotation(String displayChar, String desc,
char secondaryStructure, float val, Color color)
{
- return new Annotation(displayChar, desc, secondaryStructure, val, color);
+ return new Annotation(displayChar, desc, secondaryStructure, val,
+ color);
}
/**
* @param af
* @param counter
*/
- public AnnotationWorker(AlignViewportI viewport,
- AlignmentViewPanel panel, AnnotationProviderI counter)
+ public AnnotationWorker(AlignViewportI viewport, AlignmentViewPanel panel,
+ AnnotationProviderI counter)
{
super(viewport, panel);
ourAnnots = new ArrayList<AlignmentAnnotation>();
}
while (!calcMan.notifyWorking(this))
{
- // System.err.println("Thread (Consensus"+Thread.currentThread().getName()+") Waiting around.");
+ // System.err.println("Thread
+ // (Consensus"+Thread.currentThread().getName()+") Waiting around.");
try
{
if (ap != null)
{
// Deal with Transaction exceptions
wsInfo.appendProgressText(jobs[j].jobnum, MessageManager
- .formatMessage("info.server_exception", new Object[] {
- WebServiceName, ex.getMessage() }));
+ .formatMessage("info.server_exception", new Object[]
+ { WebServiceName, ex.getMessage() }));
// always output the exception's stack trace to the log
Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
+ ") Server exception.");
WebserviceInfo.STATE_STOPPED_ERROR);
Cache.log.error("Out of memory when retrieving Job " + j
+ " id:" + WsUrl + "/" + jobs[j].jobId, er);
- new jalview.gui.OOMWarning("retrieving result for "
- + WebServiceName, er);
+ new jalview.gui.OOMWarning(
+ "retrieving result for " + WebServiceName, er);
System.gc();
}
}
Thread.sleep(5000);
} catch (InterruptedException e)
{
- Cache.log
- .debug("Interrupted sleep waiting for next job poll.", e);
+ Cache.log.debug("Interrupted sleep waiting for next job poll.",
+ e);
}
// System.out.println("I'm alive "+alTitle);
}
}
else
{
- Cache.log
- .debug("WebServiceJob poll loop finished with no jobs created.");
+ Cache.log.debug(
+ "WebServiceJob poll loop finished with no jobs created.");
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
- wsInfo.appendProgressText(MessageManager
- .getString("info.no_jobs_ran"));
+ wsInfo.appendProgressText(
+ MessageManager.getString("info.no_jobs_ran"));
wsInfo.setFinishedNoResults();
}
}
// af.featureSettings_actionPerformed(null);
String[] defdb = null;
List<DbSourceProxy> selsources = new ArrayList<DbSourceProxy>();
- Vector<jalviewSourceI> dasselsrc = (featureSettings != null) ? featureSettings
- .getSelectedSources() : new DasSourceBrowser()
- .getSelectedSources();
+ Vector<jalviewSourceI> dasselsrc = (featureSettings != null)
+ ? featureSettings.getSelectedSources()
+ : new DasSourceBrowser().getSelectedSources();
for (jalviewSourceI src : dasselsrc)
{
DbSourceProxy[] newsrc = new DbSourceProxy[dbSources.length
+ otherdb.length];
System.arraycopy(dbSources, 0, newsrc, 0, dbSources.length);
- System.arraycopy(otherdb, 0, newsrc, dbSources.length, otherdb.length);
+ System.arraycopy(otherdb, 0, newsrc, dbSources.length,
+ otherdb.length);
dbSources = newsrc;
}
}
{
if (dbSources == null)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_must_init_dbsources"));
+ throw new Error(MessageManager
+ .getString("error.implementation_error_must_init_dbsources"));
}
running = true;
long startTime = System.currentTimeMillis();
String query = queries.elementAt(0);
if (dbsource.isValidReference(query))
{
- queryString.append((numq == 0) ? "" : dbsource
- .getAccessionSeparator());
+ queryString.append(
+ (numq == 0) ? "" : dbsource.getAccessionSeparator());
queryString.append(query);
numq++;
}
else
{
// make some more strings for use as queries
- for (int i = 0; (seqIndex < dataset.length) && (i < 50); seqIndex++, i++)
+ for (int i = 0; (seqIndex < dataset.length)
+ && (i < 50); seqIndex++, i++)
{
SequenceI sequence = dataset[seqIndex];
- DBRefEntry[] uprefs = DBRefUtils.selectRefs(
- sequence.getDBRefs(),
- new String[] { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
+ DBRefEntry[] uprefs = DBRefUtils
+ .selectRefs(sequence.getDBRefs(), new String[]
+ { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
// });
// check for existing dbrefs to use
if (uprefs != null && uprefs.length > 0)
for (int j = 0; j < uprefs.length; j++)
{
addSeqId(sequence, uprefs[j].getAccessionId());
- queries.addElement(uprefs[j].getAccessionId().toUpperCase());
+ queries.addElement(
+ uprefs[j].getAccessionId().toUpperCase());
}
}
else
// resolve the string against PICR to recover valid IDs
try
{
- presp = picrClient
- .getUPIForAccession(token, null,
- picrClient.getMappedDatabaseNames(),
- null, true);
+ presp = picrClient.getUPIForAccession(token, null,
+ picrClient.getMappedDatabaseNames(), null,
+ true);
} catch (Exception e)
{
- System.err.println("Exception with Picr for '" + token
- + "'\n");
+ System.err.println(
+ "Exception with Picr for '" + token + "'\n");
e.printStackTrace();
}
}
// present, and do a transferReferences
// otherwise transfer non sequence x-references directly.
}
- System.out
- .println("Validated ID against PICR... (for what its worth):"
+ System.out.println(
+ "Validated ID against PICR... (for what its worth):"
+ token);
addSeqId(sequence, token);
queries.addElement(token.toUpperCase());
else
{
// if ()
- // System.out.println("Not querying source with token="+token+"\n");
+ // System.out.println("Not querying source with
+ // token="+token+"\n");
addSeqId(sequence, token);
queries.addElement(token.toUpperCase());
}
output.setText(sb.toString());
Desktop.addInternalFrame(output,
- MessageManager.getString("label.sequences_updated"), 600, 300);
+ MessageManager.getString("label.sequences_updated"), 600,
+ 300);
// The above is the dataset, we must now find out the index
// of the viewed sequence
}
boolean modified = false;
- SequenceI[] retrieved = recoverDbSequences(retrievedAl
- .getSequencesArray());
+ SequenceI[] retrieved = recoverDbSequences(
+ retrievedAl.getSequencesArray());
SequenceI sequence = null;
for (SequenceI retrievedSeq : retrieved)
// taking into account all accessionIds and names in the file
Vector<SequenceI> sequenceMatches = new Vector<SequenceI>();
// look for corresponding accession ids
- DBRefEntry[] entryRefs = DBRefUtils.selectRefs(
- retrievedSeq.getDBRefs(), new String[] { dbSource });
+ DBRefEntry[] entryRefs = DBRefUtils
+ .selectRefs(retrievedSeq.getDBRefs(), new String[]
+ { dbSource });
if (entryRefs == null)
{
System.err
final int sequenceStart = sequence.getStart();
boolean remoteEnclosesLocal = false;
- String nonGapped = AlignSeq.extractGaps("-. ",
- sequence.getSequenceAsString()).toUpperCase();
+ String nonGapped = AlignSeq
+ .extractGaps("-. ", sequence.getSequenceAsString())
+ .toUpperCase();
int absStart = entrySeq.indexOf(nonGapped);
if (absStart == -1)
{
* So create a mapping to the external entry from the matching region of
* the local sequence, and leave local start/end untouched.
*/
- mp = new Mapping(null, new int[] { sequenceStart + absStart,
- sequenceStart + absStart + entrySeq.length() - 1 }, new int[]
- { retrievedSeq.getStart(),
- retrievedSeq.getStart() + entrySeq.length() - 1 }, 1, 1);
+ mp = new Mapping(null,
+ new int[]
+ { sequenceStart + absStart,
+ sequenceStart + absStart + entrySeq.length() - 1 },
+ new int[]
+ { retrievedSeq.getStart(),
+ retrievedSeq.getStart() + entrySeq.length() - 1 },
+ 1, 1);
updateRefFrame = false;
}
else
sequence.setSequence(retrievedSeqString);
modified = true;
addWarningMessage(warningMessages,
- "Sequence for " + sequence.getName()
- + " expanded from " + retrievedSeq.getName());
+ "Sequence for " + sequence.getName() + " expanded from "
+ + retrievedSeq.getName());
}
if (sequence.getStart() != retrievedSeq.getStart())
{
modified = true;
if (absStart != sequenceStart)
{
- addWarningMessage(warningMessages, "Start/end position for "
- + sequence.getName() + " updated from "
- + retrievedSeq.getName());
+ addWarningMessage(warningMessages,
+ "Start/end position for " + sequence.getName()
+ + " updated from " + retrievedSeq.getName());
}
}
}
sequence.setStart(absStart);
sequence.setEnd(absEnd);
modified = true;
- addWarningMessage(warningMessages, "Start/end for "
- + sequence.getName() + " updated from "
- + retrievedSeq.getName());
+ addWarningMessage(warningMessages,
+ "Start/end for " + sequence.getName()
+ + " updated from " + retrievedSeq.getName());
}
}
// search for alignment sequences to update coordinate frame for
{
if (alseqs[alsq].getDatasetSequence() == sequence)
{
- String ngAlsq = AlignSeq.extractGaps("-. ",
- alseqs[alsq].getSequenceAsString()).toUpperCase();
+ String ngAlsq = AlignSeq
+ .extractGaps("-. ",
+ alseqs[alsq].getSequenceAsString())
+ .toUpperCase();
int oldstrt = alseqs[alsq].getStart();
alseqs[alsq].setStart(sequence.getSequenceAsString()
- .toUpperCase().indexOf(ngAlsq)
- + sequence.getStart());
+ .toUpperCase().indexOf(ngAlsq) + sequence.getStart());
if (oldstrt != alseqs[alsq].getStart())
{
- alseqs[alsq].setEnd(ngAlsq.length()
- + alseqs[alsq].getStart() - 1);
+ alseqs[alsq].setEnd(
+ ngAlsq.length() + alseqs[alsq].getStart() - 1);
modified = true;
}
}
private SequenceI[] recoverDbSequences(SequenceI[] sequencesArray)
{
Vector<SequenceI> nseq = new Vector<SequenceI>();
- for (int i = 0; sequencesArray != null && i < sequencesArray.length; i++)
+ for (int i = 0; sequencesArray != null
+ && i < sequencesArray.length; i++)
{
nseq.addElement(sequencesArray[i]);
DBRefEntry[] dbr = sequencesArray[i].getDBRefs();
int reply = JvOptionPane.YES_OPTION;
if (promptFetchDbrefs)
{
- reply = JvOptionPane
- .showInternalConfirmDialog(
- Desktop.desktop,
- MessageManager
- .getString("info.you_want_jalview_to_find_uniprot_accessions"),
- MessageManager
- .getString("label.find_uniprot_accession_ids"),
- JvOptionPane.YES_NO_OPTION,
- JvOptionPane.QUESTION_MESSAGE);
+ reply = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ MessageManager.getString(
+ "info.you_want_jalview_to_find_uniprot_accessions"),
+ MessageManager
+ .getString("label.find_uniprot_accession_ids"),
+ JvOptionPane.YES_NO_OPTION, JvOptionPane.QUESTION_MESSAGE);
}
if (reply == JvOptionPane.YES_OPTION)
startTime = System.currentTimeMillis();
if (af != null)
{
- af.setProgressBar(MessageManager
- .getString("status.fetching_das_sequence_features"),
- startTime);
+ af.setProgressBar(MessageManager.getString(
+ "status.fetching_das_sequence_features"), startTime);
}
if (sourceRegistry == null)
{
{
try
{
- jalviewSourceI[] sources = sourceRegistry.getSources().toArray(
- new jalviewSourceI[0]);
+ jalviewSourceI[] sources = sourceRegistry.getSources()
+ .toArray(new jalviewSourceI[0]);
String active = Cache.getDefault("DAS_ACTIVE_SOURCE", "uniprot");
StringTokenizer st = new StringTokenizer(active, "\t");
selectedSources = new Vector();
for (List<String> idl : ids)
{
String source = sources.next();
- FeaturesClient featuresc = new FeaturesClient(sourceRegistry
- .getSessionHandler().getConnectionPropertyProviderFor(
- source));
+ FeaturesClient featuresc = new FeaturesClient(
+ sourceRegistry.getSessionHandler()
+ .getConnectionPropertyProviderFor(source));
for (String id : idl)
{
List<String> qid = Arrays.asList(new String[] { id });
}
private void processResponse(Map<String, SequenceI> sequencemap,
- jalviewSourceI jvsource, List<String> ids,
- List<DBRefEntry> idobj, Map<List<String>, DasGFFAdapter> results,
+ jalviewSourceI jvsource, List<String> ids, List<DBRefEntry> idobj,
+ Map<List<String>, DasGFFAdapter> results,
Map<List<String>, Exception> errors)
{
Set<SequenceI> sequences = new HashSet<SequenceI>();
vf = dbref.getMap().locateFeature(f);
} catch (Exception ex)
{
- Cache.log
- .warn("Error in 'experimental' mapping of features. Please try to reproduce and then report info to jalview-discuss@jalview.org.");
+ Cache.log.warn(
+ "Error in 'experimental' mapping of features. Please try to reproduce and then report info to jalview-discuss@jalview.org.");
Cache.log.warn("Mapping feature from " + f.getBegin()
+ " to " + f.getEnd() + " in dbref "
+ dbref.getAccessionId() + " in "
{
if (af != null)
{
- af.setProgressBar(MessageManager
- .getString("status.das_feature_fetching_cancelled"),
- startTime);
+ af.setProgressBar(MessageManager.getString(
+ "status.das_feature_fetching_cancelled"), startTime);
}
cancelled = true;
}
if (!cancelled && af != null)
{
// only update the progress bar if we've completed the fetch normally
- af.setProgressBar(MessageManager
- .getString("status.das_feature_fetching_complete"), startTime);
+ af.setProgressBar(MessageManager.getString(
+ "status.das_feature_fetching_complete"), startTime);
}
if (af != null && af.featureSettings != null)
return null;
}
DBRefEntry[] uprefs = DBRefUtils.selectRefs(seq.getDBRefs(),
- new String[] {
- // jalview.datamodel.DBRefSource.PDB,
- DBRefSource.UNIPROT,
+ new String[]
+ {
+ // jalview.datamodel.DBRefSource.PDB,
+ DBRefSource.UNIPROT,
// jalview.datamodel.DBRefSource.EMBL - not tested on any EMBL coord
// sys sources
});
// - the start/end for the DBRefEntry may not be the same as the
// sequence's start/end
- System.out.println(seq.getName() + " "
- + (seq.getDatasetSequence() == null) + " "
- + csys.getUri());
+ System.out.println(
+ seq.getName() + " " + (seq.getDatasetSequence() == null)
+ + " " + csys.getUri());
dasCoordSysFound = true; // break's out of the loop
ids.add(uprefs[j]);
{
}
- SequenceFeature f = new SequenceFeature(
- getTypeString(feat.getTYPE()), desc, start, end, score,
- nickname);
+ SequenceFeature f = new SequenceFeature(getTypeString(feat.getTYPE()),
+ desc, start, end, score, nickname);
if (feat.getLINK() != null)
{
HttpVersion.HTTP_1_1);
if (connectionTimeoutMs > 0)
{
- HttpConnectionParams
- .setConnectionTimeout(params, connectionTimeoutMs);
+ HttpConnectionParams.setConnectionTimeout(params,
+ connectionTimeoutMs);
}
if (readTimeoutMs > 0)
{
if (resEntity != null)
{
- BufferedReader r = new BufferedReader(new InputStreamReader(
- resEntity.getContent()));
+ BufferedReader r = new BufferedReader(
+ new InputStreamReader(resEntity.getContent()));
return r;
}
else
mpe.addPart(nvp.getName(), new StringBody(nvp.getValue()));
}
- FileBody fb = new FileBody(file, mtype != null ? mtype
- : "application/octet-stream");
+ FileBody fb = new FileBody(file,
+ mtype != null ? mtype : "application/octet-stream");
mpe.addPart(fparm, fb);
UrlEncodedFormEntity ue = new UrlEncodedFormEntity(vals, "UTF-8");
httppost.setEntity(ue);
if (resEntity != null)
{
- BufferedReader r = new BufferedReader(new InputStreamReader(
- resEntity.getContent()));
+ BufferedReader r = new BufferedReader(
+ new InputStreamReader(resEntity.getContent()));
return r;
}
else
public static BufferedReader doHttpMpartInputstreamPost(String postUrl,
List<NameValuePair> vals, String fparm, String fname,
- InputStream is, String mtype) throws ClientProtocolException,
- IOException
+ InputStream is, String mtype)
+ throws ClientProtocolException, IOException
{
HttpClient httpclient = new DefaultHttpClient();
HttpPost httppost = new HttpPost(postUrl);
mpe.addPart(nvp.getName(), new StringBody(nvp.getValue()));
}
- InputStreamBody fb = (mtype != null) ? new InputStreamBody(is, fname,
- mtype) : new InputStreamBody(is, fname);
+ InputStreamBody fb = (mtype != null)
+ ? new InputStreamBody(is, fname, mtype)
+ : new InputStreamBody(is, fname);
mpe.addPart(fparm, fb);
UrlEncodedFormEntity ue = new UrlEncodedFormEntity(vals, "UTF-8");
httppost.setEntity(ue);
if (resEntity != null)
{
- BufferedReader r = new BufferedReader(new InputStreamReader(
- resEntity.getContent()));
+ BufferedReader r = new BufferedReader(
+ new InputStreamReader(resEntity.getContent()));
return r;
}
else
{
serror++;
j.subjobComplete = true;
- wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR);
+ wsInfo.setStatus(j.jobnum,
+ WebserviceInfo.STATE_STOPPED_SERVERERROR);
}
else if (j.isBroken())
{
}
// } catch (OutOfMemoryError e)
// {
- // System.err.println("Out of memory when displaying status. Squashing error.");
+ // System.err.println("Out of memory when displaying status. Squashing
+ // error.");
// wsInfo.appendProgressText(j.jobnum,
// "..\n(Out of memory when displaying status)\n");
// }
public String[] getOrderedSupportedSources()
{
String[] srcs = this.getSupportedDb();
- ArrayList<String> dassrc = new ArrayList<String>(), nondas = new ArrayList<String>();
+ ArrayList<String> dassrc = new ArrayList<String>(),
+ nondas = new ArrayList<String>();
for (int i = 0; i < srcs.length; i++)
{
boolean das = false, skip = false;
else
{
nm = dbs.getDbName();
- if (getSourceProxy(srcs[i]) instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
+ if (getSourceProxy(
+ srcs[i]) instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
{
if (nm.startsWith("das:"))
{
nondas.add(srcs[i]);
}
}
- String[] tosort = nondas.toArray(new String[0]), sorted = nondas
- .toArray(new String[0]);
+ String[] tosort = nondas.toArray(new String[0]),
+ sorted = nondas.toArray(new String[0]);
for (int j = 0, jSize = sorted.length; j < jSize; j++)
{
tosort[j] = tosort[j].toLowerCase();
{
stopQuery();
throw new Exception(MessageManager.formatMessage(
- "exception.ebiembl_retrieval_failed_on", new String[] {
- emprefx.toLowerCase(), query.trim() }), e);
+ "exception.ebiembl_retrieval_failed_on", new String[]
+ { emprefx.toLowerCase(), query.trim() }), e);
}
return getEmblSequenceRecords(emprefx, query, reply);
}
// todo get rid of Type and use FileFormatI instead?
FileFormatI fileFormat = (pdbFileFormat == Type.PDB) ? FileFormat.PDB
: FileFormat.MMCif;
- pdbAlignment = new FormatAdapter().readFile(file,
- DataSourceType.FILE, fileFormat);
+ pdbAlignment = new FormatAdapter().readFile(file, DataSourceType.FILE,
+ fileFormat);
if (pdbAlignment != null)
{
List<SequenceI> toremove = new ArrayList<SequenceI>();
}
}
- if (chain == null
- || (chid != null && (chid.equals(chain)
- || chid.trim().equals(chain.trim()) || (chain
- .trim().length() == 0 && chid.equals("_")))))
+ if (chain == null || (chid != null && (chid.equals(chain)
+ || chid.trim().equals(chain.trim())
+ || (chain.trim().length() == 0 && chid.equals("_")))))
{
// FIXME seems to result in 'PDB|1QIP|1qip|A' - 1QIP is redundant.
// TODO: suggest simplify naming to 1qip|A as default name defined
- pdbcs.setName(jalview.datamodel.DBRefSource.PDB + SEPARATOR
- + id + SEPARATOR + pdbcs.getName());
+ pdbcs.setName(jalview.datamodel.DBRefSource.PDB + SEPARATOR + id
+ + SEPARATOR + pdbcs.getName());
// Might need to add more metadata to the PDBEntry object
// like below
/*
if (pdbAlignment == null || pdbAlignment.getHeight() < 1)
{
throw new Exception(MessageManager.formatMessage(
- "exception.no_pdb_records_for_chain", new String[] { id,
- ((chain == null) ? "' '" : chain) }));
+ "exception.no_pdb_records_for_chain", new String[]
+ { id, ((chain == null) ? "' '" : chain) }));
}
} catch (Exception ex) // Problem parsing PDB file
{
return "/alignment/full";
}
+
/*
* (non-Javadoc)
*
{
return "/alignment/seed";
}
+
/*
* (non-Javadoc)
*
{
return "/alignment/full";
}
+
/*
* (non-Javadoc)
*
// uniprotkb dbname changed introduced december 2008
File file = ebi.fetchDataAsFile("uniprotkb:" + queries, "uniprotxml",
"xml");
- Vector<UniprotEntry> entries = getUniprotEntries(new FileReader(file));
+ Vector<UniprotEntry> entries = getUniprotEntries(
+ new FileReader(file));
if (entries != null)
{
public SequenceI uniprotEntryToSequenceI(UniprotEntry entry)
{
String id = getUniprotEntryId(entry);
- SequenceI sequence = new Sequence(id, entry.getUniprotSequence()
- .getContent());
+ SequenceI sequence = new Sequence(id,
+ entry.getUniprotSequence().getContent());
sequence.setDescription(getUniprotEntryDescription(entry));
final String dbVersion = getDbVersion();
String cdsId = (String) pdb.getProperty("protein sequence ID");
if (cdsId != null && cdsId.trim().length() > 0)
{
- dbr = new DBRefEntry(DBRefSource.ENSEMBL, DBRefSource.UNIPROT
- + ":" + dbVersion, cdsId.trim());
+ dbr = new DBRefEntry(DBRefSource.ENSEMBL,
+ DBRefSource.UNIPROT + ":" + dbVersion, cdsId.trim());
dbRefs.add(dbr);
}
// retrieved.
startQuery();
// TODO: trap HTTP 404 exceptions and return null
- String xfamUrl = getXFAMURL()
- + queries.trim().toUpperCase() + getXFAMURLSUFFIX();
+ String xfamUrl = getXFAMURL() + queries.trim().toUpperCase()
+ + getXFAMURLSUFFIX();
if (Cache.log != null)
{
Cache.log.debug("XFAM URL for retrieval is: " + xfamUrl);
}
- AlignmentI rcds = new FormatAdapter().readFile(xfamUrl ,
+ AlignmentI rcds = new FormatAdapter().readFile(xfamUrl,
DataSourceType.URL, FileFormat.Stockholm);
for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
{
rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getXfamSource(),
- // getDbSource(),
+ // getDbSource(),
getDbVersion(), queries.trim().toUpperCase()));
if (!getDbSource().equals(getXfamSource()))
{ // add the specific ref too
- rcds.getSequenceAt(s).addDBRef(
- new DBRefEntry(getDbSource(), getDbVersion(), queries
- .trim().toUpperCase()));
+ rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getDbSource(),
+ getDbVersion(), queries.trim().toUpperCase()));
}
}
stopQuery();
* @author JimP
*
*/
-public class DasSequenceSource extends DbSourceProxyImpl implements
- DbSourceProxy
+public class DasSequenceSource extends DbSourceProxyImpl
+ implements DbSourceProxy
{
private jalviewSourceI jsrc;
{
throw new Exception(MessageManager.formatMessage(
"exception.das_source_doesnt_support_sequence_command",
- new String[] { source.getTitle() }));
+ new String[]
+ { source.getTitle() }));
}
this.tier = 1 + ((jsrc.isLocal() || jsrc.isReferenceSource()) ? 0 : 1);
this.source = source;
public AlignmentI getSequenceRecords(String queries) throws Exception
{
StringTokenizer st = new StringTokenizer(queries, "\t");
- List<String> toks = new ArrayList<String>(), src = new ArrayList<String>(), acIds = new ArrayList<String>();
+ List<String> toks = new ArrayList<String>(),
+ src = new ArrayList<String>(), acIds = new ArrayList<String>();
while (st.hasMoreTokens())
{
String t;
// slow, fetch one at a time.
for (String sr : src)
{
- System.err
- .println("Retrieving IDs individually from das source: "
- + sr);
+ System.err.println(
+ "Retrieving IDs individually from das source: " + sr);
org.biodas.jdas.client.SequenceClient sq = new SequenceClient(
connprops.getConnectionPropertyProviderFor(sr));
for (String q : toks)
Map<List<String>, DasSequenceAdapter> dss = resultset.get(sr);
if (dss == null)
{
- resultset
- .put(sr,
- dss = new HashMap<List<String>, DasSequenceAdapter>());
+ resultset.put(sr,
+ dss = new HashMap<List<String>, DasSequenceAdapter>());
}
dss.put(qset, s);
} catch (Exception x)
Map<List<String>, Exception> ers = errors.get(sr);
if (ers == null)
{
- errors.put(sr, ers = new HashMap<List<String>, Exception>());
+ errors.put(sr,
+ ers = new HashMap<List<String>, Exception>());
}
ers.put(qset, x);
}
if (acIds.indexOf(lbl) == -1)
{
- System.err
- .println("Warning - received sequence event for strange accession code ("
+ System.err.println(
+ "Warning - received sequence event for strange accession code ("
+ lbl + ")");
}
else
{
if (e.getContent().length() == 0)
{
- System.err
- .println("Empty sequence returned for accession code ("
- + lbl
- + ") from "
- + resset.getKey()
+ System.err.println(
+ "Empty sequence returned for accession code ("
+ + lbl + ") from " + resset.getKey()
+ " (source is " + getDbName());
continue;
}
seqs = new java.util.Vector<SequenceI>();
// JDAS returns a sequence complete with any newlines and spaces
// in the XML
- Sequence sq = new Sequence(lbl, e.getContent().replaceAll(
- "\\s+", ""));
+ Sequence sq = new Sequence(lbl,
+ e.getContent().replaceAll("\\s+", ""));
sq.setStart(e.getStart().intValue());
- sq.addDBRef(new DBRefEntry(getDbSource(), getDbVersion()
- + ":" + e.getVersion(), lbl));
+ sq.addDBRef(new DBRefEntry(getDbSource(),
+ getDbVersion() + ":" + e.getVersion(), lbl));
seqs.addElement(sq);
}
}
} catch (Exception x)
{
- Cache.log
- .error("Couldn't retrieve features for sequence from its source.",
- x);
+ Cache.log.error(
+ "Couldn't retrieve features for sequence from its source.",
+ x);
}
}
/**
*
*/
-public class DasSourceRegistry implements DasSourceRegistryI,
- MultipleConnectionPropertyProviderI
+public class DasSourceRegistry
+ implements DasSourceRegistryI, MultipleConnectionPropertyProviderI
{
// private org.biodas.jdas.schema.sources.SOURCE[] dasSources = null;
private List<jalviewSourceI> dasSources = null;
if (registry.lastIndexOf("sources.xml") == registry.length() - 11)
{
// no trailing sources.xml document for registry in JDAS
- jalview.bin.Cache.setProperty(
- jalview.bin.Cache.DAS_REGISTRY_URL,
+ jalview.bin.Cache.setProperty(jalview.bin.Cache.DAS_REGISTRY_URL,
registry = registry.substring(0,
registry.lastIndexOf("sources.xml")));
}
}
else
{
- System.out.println("Debug: Ignored older source "
- + jsrc.getTitle());
+ System.out.println(
+ "Debug: Ignored older source " + jsrc.getTitle());
}
}
else
return dsrc;
} catch (Exception ex)
{
- System.out.println("DAS1 registry at " + registryURL
- + " no longer exists");
+ System.out.println(
+ "DAS1 registry at " + registryURL + " no longer exists");
return new ArrayList<jalviewSourceI>();
}
}
int bar = token.indexOf("|");
if (bar == -1)
{
- System.err
- .println("Warning: DAS user local source appears to have no nickname (expected a '|' followed by nickname)\nOffending definition: '"
+ System.err.println(
+ "Warning: DAS user local source appears to have no nickname (expected a '|' followed by nickname)\nOffending definition: '"
+ token + "'");
}
String url = token.substring(bar + 1);
}
} catch (Exception q)
{
- System.err
- .println("Unexpected exception when creating local source from '"
+ System.err.println(
+ "Unexpected exception when creating local source from '"
+ token + "'");
q.printStackTrace();
}
{
String token = en.nextElement().toString();
jalviewSourceI srco = localSources.get(token);
- sb.append(token + "|"
- + (srco.isSequenceSource() ? "sequence:" : "")
+ sb.append(token + "|" + (srco.isSequenceSource() ? "sequence:" : "")
+ srco.getUri() + "\t");
}
return sb.toString();
try
{
// TODO: allow same credentials for https and http
- authStash.put(new URL(
- "http://www.compbio.dundee.ac.uk/geneweb/das/myseq/"),
+ authStash.put(
+ new URL("http://www.compbio.dundee.ac.uk/geneweb/das/myseq/"),
"Basic SmltOm1pSg==");
} catch (MalformedURLException e)
{
{
for (CAPABILITY p : getVersion().getCAPABILITY())
{
- if (p.getType().equalsIgnoreCase(capability.getName())
- || p.getType().equalsIgnoreCase(
- "das1:" + capability.getName()))
+ if (p.getType().equalsIgnoreCase(capability.getName()) || p.getType()
+ .equalsIgnoreCase("das1:" + capability.getName()))
{
return p;
}
for (COORDINATES cs : v.getCOORDINATES())
{
COORDINATES ltst = latestc.get(cs.getUri());
- if (ltst == null
- || ltst.getVersion() == null
- || (ltst.getVersion() != null && cs.getVersion() != null && isLaterThan(
- ltst.getVersion(), cs.getVersion())))
+ if (ltst == null || ltst.getVersion() == null
+ || (ltst.getVersion() != null && cs.getVersion() != null
+ && isLaterThan(ltst.getVersion(), cs.getVersion())))
{
latestc.put(cs.getUri(), cs);
}
*/
try
{
- seqsources.add(ds = new DasSequenceSource(getTitle() + " ("
- + cs.getAuthority() + " " + cs.getSource()
- + (cs.getVersion() != null ? " " + cs.getVersion() : "")
- + ")", cs.getAuthority(), source, v, cs, connprov));
+ seqsources.add(ds = new DasSequenceSource(
+ getTitle() + " (" + cs.getAuthority() + " "
+ + cs.getSource()
+ + (cs.getVersion() != null ? " " + cs.getVersion()
+ : "")
+ + ")",
+ cs.getAuthority(), source, v, cs, connprov));
if (seqsources.size() > 1)
{
System.err.println("Added another sequence DB source for "
{
try
{
- seqsources.add(new DasSequenceSource(getTitle(), getTitle(),
- source, getVersion(), null, connprov));
+ seqsources.add(new DasSequenceSource(getTitle(), getTitle(), source,
+ getVersion(), null, connprov));
} catch (Exception e)
{
// TODO Auto-generated catch block
for (CAPABILITY cap : getVersion().getCAPABILITY())
{
- String capname = cap.getType().substring(
- cap.getType().indexOf(":") + 1);
+ String capname = cap.getType()
+ .substring(cap.getType().indexOf(":") + 1);
int p = cap.getQueryUri().lastIndexOf(capname);
if (p < -1)
{
throw new Exception(MessageManager.formatMessage(
- "exception.invalid_das_source",
- new String[] { source.getUri() }));
+ "exception.invalid_das_source", new String[]
+ { source.getUri() }));
}
if (cap.getQueryUri().charAt(p) == '/')
{
@Override
public boolean isNewerThan(jalviewSourceI other)
{
- return isLaterThan(getVersion().getCreated(), other.getVersion()
- .getCreated());
+ return isLaterThan(getVersion().getCreated(),
+ other.getVersion().getCreated());
}
@Override
AlignmentI al = null;
while (r.hasNext())
{
- FileParse fp = new InputStreamParser(r.next(), source.getDataName());
+ FileParse fp = new InputStreamParser(r.next(),
+ source.getDataName());
AlignmentI nal = new FormatAdapter().readFromFile(fp,
FileFormat.Rnaml);
if (al == null)
}
else
{
- throw new IOException(
- MessageManager
- .getString("exception.unexpected_handling_rnaml_translation_for_pdb"),
+ throw new IOException(MessageManager.getString(
+ "exception.unexpected_handling_rnaml_translation_for_pdb"),
x);
}
}
URL url = new URL(
"http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="
+ content);
- BufferedReader is = new BufferedReader(new InputStreamReader(
- url.openStream()));
+ BufferedReader is = new BufferedReader(
+ new InputStreamReader(url.openStream()));
String str4;
while ((str4 = is.readLine()) != null)
{
// timeout
} catch (Exception ex)
{
- jalview.bin.Cache.log
- .error("Serious! Service location failed\nfor URL :" + WsURL
- + "\n", ex);
+ jalview.bin.Cache.log.error(
+ "Serious! Service location failed\nfor URL :" + WsURL + "\n",
+ ex);
return null;
}
static private Vector getDiscoveryURLS()
{
Vector urls = new Vector();
- String RootServiceURLs = jalview.bin.Cache
- .getDefault("DISCOVERY_URLS",
- "http://www.compbio.dundee.ac.uk/JalviewWS/services/ServiceRegistry");
+ String RootServiceURLs = jalview.bin.Cache.getDefault("DISCOVERY_URLS",
+ "http://www.compbio.dundee.ac.uk/JalviewWS/services/ServiceRegistry");
try
{
jalview.bin.Cache.log
.warn("Problem whilst trying to make a URL from '"
+ ((url != null) ? url : "<null>") + "'");
- jalview.bin.Cache.log
- .warn("This was probably due to a malformed comma separated list"
+ jalview.bin.Cache.log.warn(
+ "This was probably due to a malformed comma separated list"
+ " in the DISCOVERY_URLS entry of $(HOME)/.jalview_properties)");
jalview.bin.Cache.log.debug("Exception was ", ex);
}
}
} catch (Exception ex)
{
- jalview.bin.Cache.log
- .warn("Error parsing comma separated list of urls in DISCOVERY_URLS.",
- ex);
+ jalview.bin.Cache.log.warn(
+ "Error parsing comma separated list of urls in DISCOVERY_URLS.",
+ ex);
}
if (urls.size() > 0)
{
.debug("(Re)-Initialising the discovery URL list.");
try
{
- reallyDiscoverServices = jalview.bin.Cache.getDefault(
- "DISCOVERY_START", false);
+ reallyDiscoverServices = jalview.bin.Cache
+ .getDefault("DISCOVERY_START", false);
if (reallyDiscoverServices)
{
ServiceURLList = getDiscoveryURLS();
jalview.bin.Cache.log.debug("Setting default services");
services = new Hashtable();
// Muscle, Clustal and JPred.
- ServiceHandle[] defServices = {
- new ServiceHandle(
- "MsaWS",
- "Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment "
- + "with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.",
- "http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS",
- MessageManager
- .getString("label.muscle_multiple_protein_sequence_alignment")),
- new ServiceHandle(
- "MsaWS",
+ ServiceHandle[] defServices = { new ServiceHandle("MsaWS",
+ "Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment "
+ + "with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.",
+ "http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS",
+ MessageManager.getString(
+ "label.muscle_multiple_protein_sequence_alignment")),
+ new ServiceHandle("MsaWS",
"Katoh, K., K. Kuma, K., Toh, H., and Miyata, T. (2005) "
+ "\"MAFFT version 5: improvement in accuracy of multiple sequence alignment.\""
+ " Nucleic Acids Research, 33 511-518",
"http://www.compbio.dundee.ac.uk/JalviewWS/services/MafftWS",
- MessageManager
- .getString("label.mafft_multiple_sequence_alignment")),
- new ServiceHandle(
- "MsaWS",
+ MessageManager.getString(
+ "label.mafft_multiple_sequence_alignment")),
+ new ServiceHandle("MsaWS",
"Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple"
+ " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."
+ " Nucleic Acids Research, 22 4673-4680",
"http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS",
- MessageManager
- .getString("label.clustalw_multiple_sequence_alignment")),
- new ServiceHandle(
- "SecStrPred",
+ MessageManager.getString(
+ "label.clustalw_multiple_sequence_alignment")),
+ new ServiceHandle("SecStrPred",
"Drozdetskiy A, Cole C, Procter J & Barton GJ. (2015)\nJPred4: a protein secondary structure prediction server"
+ "\nNucleic Acids Research, Web Server issue (first published 15th April 2015)"
+ "\ndoi://10.1093/nar/gkv332",
} catch (Exception e)
{
- System.err
- .println("jalview.rootRegistry is not a proper url!\nWas set to "
+ System.err.println(
+ "jalview.rootRegistry is not a proper url!\nWas set to "
+ RootServiceURL + "\n" + e);
}
disc_serv = new java.net.URL(sh[i].getEndpointURL());
if (!ServiceURLList.contains(disc_serv))
{
- jalview.bin.Cache.log
- .debug("Adding new discovery service at "
- + disc_serv);
+ jalview.bin.Cache.log.debug(
+ "Adding new discovery service at " + disc_serv);
ServiceURLList.add(disc_serv);
seenNewDiscovery = true;
}
} catch (Exception e)
{
- jalview.bin.Cache.log.debug(
- "Ignoring bad discovery service URL "
+ jalview.bin.Cache.log
+ .debug("Ignoring bad discovery service URL "
+ sh[i].getEndpointURL(), e);
}
}
}
while (s_url < ServiceURLList.size())
{
- if ((sh = getServices((java.net.URL) ServiceURLList.get(s_url))) != null)
+ if ((sh = getServices(
+ (java.net.URL) ServiceURLList.get(s_url))) != null)
{
buildServiceLists(sh, cat, sscat);
}
else
{
- jalview.bin.Cache.log
- .warn("No services at "
- + (ServiceURLList.get(s_url))
- + " - check DISCOVERY_URLS property in .jalview_properties");
+ jalview.bin.Cache.log.warn("No services at "
+ + (ServiceURLList.get(s_url))
+ + " - check DISCOVERY_URLS property in .jalview_properties");
}
s_url++;
}
serviceClientBindings.put("SecStrPred", new JPredClient());
serviceClientBindings.put("SeqSearch", new SeqSearchWSClient());
}
- WS1Client instance = (WS1Client) serviceClientBindings.get(sh
- .getAbstractName());
+ WS1Client instance = (WS1Client) serviceClientBindings
+ .get(sh.getAbstractName());
if (instance == null)
{
- System.err
- .println("WARNING - POSSIBLE IMPLEMENTATION ERROR - cannot find WSClient implementation for "
+ System.err.println(
+ "WARNING - POSSIBLE IMPLEMENTATION ERROR - cannot find WSClient implementation for "
+ sh.getAbstractName());
}
else
* @param viewonly
* TODO
*/
- public JPredClient(ext.vamsas.ServiceHandle sh, String title,
- boolean msa, AlignmentView alview, AlignFrame parentFrame,
- boolean viewonly)
+ public JPredClient(ext.vamsas.ServiceHandle sh, String title, boolean msa,
+ AlignmentView alview, AlignFrame parentFrame, boolean viewonly)
{
super();
wsInfo = setWebService(sh);
{
if (!msa && msf.length > 1)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_multiple_single_sequence_prediction_jobs_not_supported"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_multiple_single_sequence_prediction_jobs_not_supported"));
}
String altitle = getPredictionName(WebServiceName) + " for "
private String getPredictionName(String webServiceName)
{
- if (webServiceName.toLowerCase().indexOf(
- "secondary structure prediction") > -1)
+ if (webServiceName.toLowerCase()
+ .indexOf("secondary structure prediction") > -1)
{
return webServiceName;
}
wsInfo.setProgressText("Job details for MSA based prediction (" + title
+ ") on sequence :\n>" + seq.getName() + "\n"
- + AlignSeq.extractGaps("-. ", seq.getSequenceAsString()) + "\n");
+ + AlignSeq.extractGaps("-. ", seq.getSequenceAsString())
+ + "\n");
SequenceI aln[] = new SequenceI[msf.length];
for (int i = 0, j = msf.length; i < j; i++)
{
}
wsInfo.setProgressText("Job details for prediction on sequence :\n>"
+ seq.getName() + "\n"
- + AlignSeq.extractGaps("-. ", seq.getSequenceAsString()) + "\n");
+ + AlignSeq.extractGaps("-. ", seq.getSequenceAsString())
+ + "\n");
String altitle = "JPred prediction for sequence " + seq.getName()
+ " from " + title;
} catch (Exception ex)
{
- JvOptionPane
- .showMessageDialog(
- Desktop.desktop,
- MessageManager
- .formatMessage(
- "label.secondary_structure_prediction_service_couldnt_be_located",
- new String[] { WebServiceName, WsURL }),
- MessageManager
- .getString("label.internal_jalview_error"),
- JvOptionPane.WARNING_MESSAGE);
- wsInfo.setProgressText(MessageManager
- .formatMessage(
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
"label.secondary_structure_prediction_service_couldnt_be_located",
- new String[] { WebServiceName, WsURL })
- + "\n" + ex.getMessage());
+ new String[]
+ { WebServiceName, WsURL }),
+ MessageManager.getString("label.internal_jalview_error"),
+ JvOptionPane.WARNING_MESSAGE);
+ wsInfo.setProgressText(MessageManager.formatMessage(
+ "label.secondary_structure_prediction_service_couldnt_be_located",
+ new String[]
+ { WebServiceName, WsURL }) + "\n" + ex.getMessage());
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
}
if (msa.getSequences().length == 1)
{
// Single Sequence prediction
- new jalview.ws.jws1.JPredClient(sh, af.getTitle(), false, msa,
- af, true);
+ new jalview.ws.jws1.JPredClient(sh, af.getTitle(), false, msa, af,
+ true);
}
else
{
Cache.log.debug("Parsing output from JNet job.");
// JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt",
// "File");
- JPredFile prediction = new JPredFile(
- result.getPredfile(), DataSourceType.PASTE);
+ JPredFile prediction = new JPredFile(result.getPredfile(),
+ DataSourceType.PASTE);
SequenceI[] preds = prediction.getSeqsAsArray();
Cache.log.debug("Got prediction profile.");
Cache.log.debug("Getting associated alignment.");
// we ignore the returned alignment if we only predicted on a single
// sequence
- FileFormatI format = new IdentifyFile().identify(
- result.getAligfile(), DataSourceType.PASTE);
+ FileFormatI format = new IdentifyFile()
+ .identify(result.getAligfile(), DataSourceType.PASTE);
if (format != null)
{
}
if (!SeqsetUtils.deuniquify(SequenceInfo, sqs))
{
- throw (new Exception(
- MessageManager
- .getString("exception.couldnt_recover_sequence_properties_for_alignment")));
+ throw (new Exception(MessageManager.getString(
+ "exception.couldnt_recover_sequence_properties_for_alignment")));
}
}
FirstSeq = 0;
{
al.setDataset(null);
}
- JnetAnnotationMaker.add_annotation(prediction, al,
- FirstSeq, false, predMap);
+ JnetAnnotationMaker.add_annotation(prediction, al, FirstSeq,
+ false, predMap);
}
else
{
throw (new Exception(MessageManager.formatMessage(
- "exception.unknown_format_for_file", new String[] { "",
- result.getAligfile() })));
+ "exception.unknown_format_for_file", new String[]
+ { "", result.getAligfile() })));
}
}
else
.getAlignmentAndHiddenColumns(gc)[0];
if (this.msaIndex >= sqs.length)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_invalid_msa_index_for_job"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_invalid_msa_index_for_job"));
}
// ///
// ///
new jalview.commands.RemoveGapsCommand(
MessageManager.getString("label.remove_gaps"),
- new SequenceI[] { sqs[msaIndex] }, currentView);
+ new SequenceI[]
+ { sqs[msaIndex] }, currentView);
SequenceI profileseq = al.getSequenceAt(FirstSeq);
profileseq.setSequence(sqs[msaIndex].getSequenceAsString());
if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
al.getSequenceAt(FirstSeq), SequenceInfo))
{
- throw (new Exception(
- MessageManager
- .getString("exception.couldnt_recover_sequence_props_for_jnet_query")));
+ throw (new Exception(MessageManager.getString(
+ "exception.couldnt_recover_sequence_props_for_jnet_query")));
}
else
{
dsseq = dsseq.getDatasetSequence();
}
// look for same annotation on dataset and lift this one over
- List<AlignmentAnnotation> dsan = dsseq.getAlignmentAnnotations(
- calcId, typeName);
+ List<AlignmentAnnotation> dsan = dsseq.getAlignmentAnnotations(calcId,
+ typeName);
if (dsan != null && dsan.size() > 0)
{
for (AlignmentAnnotation dssan : dsan)
sq = sq + sb;
while ((diff = gapMap[r] - sq.length()) > 0)
{
- sq = sq
- + ((diff >= sb.length()) ? sb.toString() : sb
- .substring(0, diff));
+ sq = sq + ((diff >= sb.length()) ? sb.toString()
+ : sb.substring(0, diff));
}
al.getSequenceAt(s).setSequence(sq);
}
else
{
- al.getSequenceAt(s).setSequence(
- sq.substring(0, gapMap[r]) + sb.toString()
- + sq.substring(gapMap[r]));
+ al.getSequenceAt(s).setSequence(sq.substring(0, gapMap[r])
+ + sb.toString() + sq.substring(gapMap[r]));
}
}
}
if (!(j instanceof JPredJob))
{
throw new Error(MessageManager.formatMessage(
- "error.implementation_error_startjob_called",
- new String[] { j.getClass().toString() }));
+ "error.implementation_error_startjob_called", new String[]
+ { j.getClass().toString() }));
}
try
{
{
job.result = new JpredResult();
job.result.setInvalid(true);
- job.result.setStatus(MessageManager.formatMessage(
- "label.submission_params", new String[] { job.getJobId()
- .toString() }));
+ job.result.setStatus(MessageManager
+ .formatMessage("label.submission_params", new String[]
+ { job.getJobId().toString() }));
throw new Exception(job.getJobId());
}
else
}
else
{
- throw new Exception(
- MessageManager
- .getString("exception.server_timeout_try_later"));
+ throw new Exception(MessageManager
+ .getString("exception.server_timeout_try_later"));
}
} catch (Exception e)
{
{
wsInfo.setStatus(j.getJobnum(),
WebserviceInfo.STATE_STOPPED_SERVERERROR);
- wsInfo.setProgressText(
- j.getJobnum(),
+ wsInfo.setProgressText(j.getJobnum(),
"Failed to submit the prediction. (Just close the window)\n"
+ "It is most likely that there is a problem with the server.\n");
- System.err
- .println("JPredWS Client: Failed to submit the prediction. Quite possibly because of a server error - see below)\n"
+ System.err.println(
+ "JPredWS Client: Failed to submit the prediction. Quite possibly because of a server error - see below)\n"
+ e.getMessage() + "\n");
jalview.bin.Cache.log.warn("Server Exception", e);
{
wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
// JBPNote - this could be a popup informing the user of the problem.
- wsInfo.appendProgressText(j.getJobnum(), MessageManager
- .formatMessage(
- "info.failed_to_submit_prediction",
- new String[] { e.getMessage(),
- wsInfo.getProgressText() }));
+ wsInfo.appendProgressText(j.getJobnum(),
+ MessageManager.formatMessage(
+ "info.failed_to_submit_prediction", new String[]
+ { e.getMessage(), wsInfo.getProgressText() }));
- jalview.bin.Cache.log.debug(
- "Failed Submission of job " + j.getJobnum(), e);
+ jalview.bin.Cache.log
+ .debug("Failed Submission of job " + j.getJobnum(), e);
}
j.setAllowedServerExceptions(-1);
} catch (Exception ex)
{
- Cache.log.error("Unexpected exception when processing results for "
- + altitle, ex);
+ Cache.log.error(
+ "Unexpected exception when processing results for " + altitle,
+ ex);
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
}
if (results > 0)
else
{
// do merge with other job results
- throw new Error(
- MessageManager
- .getString("error.multiple_jnet_subjob_merge_not_implemented"));
+ throw new Error(MessageManager.getString(
+ "error.multiple_jnet_subjob_merge_not_implemented"));
}
} catch (Exception e)
{
- jalview.bin.Cache.log.error(
- "JNet Client: JPred Annotation Parse Error", e);
+ jalview.bin.Cache.log
+ .error("JNet Client: JPred Annotation Parse Error", e);
wsInfo.setStatus(j.getJobnum(),
WebserviceInfo.STATE_STOPPED_ERROR);
- wsInfo.appendProgressText(j.getJobnum(), MessageManager
- .formatMessage("info.invalid_jnet_job_result_data",
- new String[] { OutputHeader.toString(),
- j.result.getStatus(), e.getMessage() }));
+ wsInfo.appendProgressText(j.getJobnum(),
+ MessageManager.formatMessage(
+ "info.invalid_jnet_job_result_data",
+ new String[]
+ { OutputHeader.toString(), j.result.getStatus(),
+ e.getMessage() }));
j.result.setBroken(true);
}
}
if (newWindow)
{
AlignFrame af;
- ((AlignmentI) res[0]).setSeqrep(((AlignmentI) res[0])
- .getSequenceAt(0));
+ ((AlignmentI) res[0])
+ .setSeqrep(((AlignmentI) res[0]).getSequenceAt(0));
if (input == null)
{
if (res[1] != null)
* alandcolsel[0])[0].gapMap())); }
*/
- af = new AlignFrame((Alignment) res[0],
- (HiddenColumns) res[1],
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ af = new AlignFrame((Alignment) res[0], (HiddenColumns) res[1],
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
}
Desktop.addInternalFrame(af, altitle, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
alignFrame = _alignFrame;
if (!sh.getAbstractName().equals("MsaWS"))
{
- JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
- .formatMessage("label.service_called_is_not_msa_service",
- new String[] { sh.getName() }), MessageManager
- .getString("label.internal_jalview_error"),
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.service_called_is_not_msa_service",
+ new String[]
+ { sh.getName() }),
+ MessageManager.getString("label.internal_jalview_error"),
JvOptionPane.WARNING_MESSAGE);
return;
if ((wsInfo = setWebService(sh)) == null)
{
JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
- .formatMessage("label.msa_service_is_unknown",
- new String[] { sh.getName() }), MessageManager
- .getString("label.internal_jalview_error"),
+ .formatMessage("label.msa_service_is_unknown", new String[]
+ { sh.getName() }),
+ MessageManager.getString("label.internal_jalview_error"),
JvOptionPane.WARNING_MESSAGE);
return;
String jobtitle = WebServiceName.toLowerCase();
if (jobtitle.endsWith("alignment"))
{
- if (submitGaps
- && (!jobtitle.endsWith("realignment") || jobtitle
- .indexOf("profile") == -1))
+ if (submitGaps && (!jobtitle.endsWith("realignment")
+ || jobtitle.indexOf("profile") == -1))
{
int pos = jobtitle.indexOf("alignment");
jobtitle = WebServiceName.substring(0, pos) + "re-alignment of "
public void actionPerformed(ActionEvent e)
{
AlignmentView msa = alignFrame.gatherSequencesForAlignment();
- new jalview.ws.jws1.MsaWSClient(serviceHandle, alignFrame
- .getTitle(), msa, false, true, alignFrame.getViewport()
- .getAlignment().getDataset(), alignFrame);
+ new jalview.ws.jws1.MsaWSClient(serviceHandle,
+ alignFrame.getTitle(), msa, false, true,
+ alignFrame.getViewport().getAlignment().getDataset(),
+ alignFrame);
}
if (canSubmitGaps())
{
// We know that ClustalWS can accept partial alignments for refinement.
- final JMenuItem methodR = new JMenuItem(serviceHandle.getName()
- + " Realign");
+ final JMenuItem methodR = new JMenuItem(
+ serviceHandle.getName() + " Realign");
methodR.setToolTipText(WsURL);
methodR.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
AlignmentView msa = alignFrame.gatherSequencesForAlignment();
- new jalview.ws.jws1.MsaWSClient(serviceHandle, alignFrame
- .getTitle(), msa, true, true, alignFrame.getViewport()
- .getAlignment().getDataset(), alignFrame);
+ new jalview.ws.jws1.MsaWSClient(serviceHandle,
+ alignFrame.getTitle(), msa, true, true,
+ alignFrame.getViewport().getAlignment().getDataset(),
+ alignFrame);
}
int nseqs = 0;
if (minlen < 0)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_minlen_must_be_greater_zero"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_minlen_must_be_greater_zero"));
}
for (int i = 0; i < seqs.length; i++)
{
}
}
boolean valid = nseqs > 1; // need at least two seqs
- vamsas.objects.simple.Sequence[] seqarray = (valid) ? new vamsas.objects.simple.Sequence[nseqs]
+ vamsas.objects.simple.Sequence[] seqarray = (valid)
+ ? new vamsas.objects.simple.Sequence[nseqs]
: null;
for (int i = 0, n = 0; i < seqs.length; i++)
{
String empty = null;
if (seqs[i].getEnd() >= seqs[i].getStart())
{
- empty = (submitGaps) ? seqs[i].getSequenceAsString() : AlignSeq
- .extractGaps(jalview.util.Comparison.GapChars,
+ empty = (submitGaps) ? seqs[i].getSequenceAsString()
+ : AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
seqs[i].getSequenceAsString());
}
emptySeqs.add(new String[] { newname, empty });
"Exception whilst cancelling " + jobs[job].getJobId(),
exc);
}
- wsInfo.setProgressText(jobs[job].getJobnum(), OutputHeader
- + cancelledMessage + "\n");
+ wsInfo.setProgressText(jobs[job].getJobnum(),
+ OutputHeader + cancelledMessage + "\n");
}
}
if (cancelled)
if (!(job instanceof MsaWSJob))
{
throw new Error(MessageManager.formatMessage(
- "error.implementation_error_msawbjob_called",
- new String[] { job.getClass().toString() }));
+ "error.implementation_error_msawbjob_called", new String[]
+ { job.getClass().toString() }));
}
MsaWSJob j = (MsaWSJob) job;
if (j.isSubmitted())
{
if (Cache.log.isDebugEnabled())
{
- Cache.log.debug("Tried to submit an already submitted job "
- + j.getJobId());
+ Cache.log.debug(
+ "Tried to submit an already submitted job " + j.getJobId());
}
return;
}
j.setSubmitted(true);
j.result = new MsaResult();
j.result.setFinished(true);
- j.result.setStatus(MessageManager
- .getString("label.empty_alignment_job"));
+ j.result.setStatus(
+ MessageManager.getString("label.empty_alignment_job"));
((MsaResult) j.result).setMsa(null);
}
try
{
throw new Exception(MessageManager.formatMessage(
"exception.web_service_returned_null_try_later",
- new String[] { WsUrl }));
+ new String[]
+ { WsUrl }));
}
throw new Exception(jobsubmit.getJobId());
{
// TODO: JBPNote catch timeout or other fault types explicitly
// For unexpected errors
- System.err
- .println(WebServiceName
- + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
- + "When contacting Server:" + WsUrl + "\n"
- + e.toString() + "\n");
+ System.err.println(WebServiceName
+ + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
+ + "When contacting Server:" + WsUrl + "\n" + e.toString()
+ + "\n");
j.setAllowedServerExceptions(0);
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
wsInfo.setStatus(j.getJobnum(),
results++;
// if (Cache.log.isDebugEnabled())
// {
- // System.out.println("Job lob for job "+jobs[j].getJobId()+":"+jobs[j].getJobnum());
+ // System.out.println("Job lob for job
+ // "+jobs[j].getJobId()+":"+jobs[j].getJobnum());
// System.out.println(jobs[j].getStatus());
// }
String[] lines = valign.getMethod();
for (int line = 0; line < lines.length; line++)
{
- wsInfo.appendProgressText(jobs[j].getJobnum(), lines[line]
- + "\n");
+ wsInfo.appendProgressText(jobs[j].getJobnum(),
+ lines[line] + "\n");
}
// JBPNote The returned files from a webservice could be
// hidden behind icons in the monitor window that,
} catch (Exception ex)
{
- Cache.log.error("Unexpected exception when processing results for "
- + alTitle, ex);
+ Cache.log.error(
+ "Unexpected exception when processing results for " + alTitle,
+ ex);
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
}
if (results > 0)
if (newFrame)
{
- AlignFrame af = new AlignFrame(al, hidden,
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ AlignFrame af = new AlignFrame(al, hidden, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
// initialise with same renderer settings as in parent alignframe.
af.getFeatureRenderer().transferSettings(this.featureSettings);
while (j < l)
{
- if (((AlignmentOrder) alorders.get(i)).equals((alorders
- .get(j))))
+ if (((AlignmentOrder) alorders.get(i))
+ .equals((alorders.get(j))))
{
alorders.remove(j);
l--;
// name to service client name
if (!sh.getAbstractName().equals(this.getServiceActionKey()))
{
- JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
- .formatMessage(
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
"label.service_called_is_not_seq_search_service",
- new String[] { sh.getName() }), MessageManager
- .getString("label.internal_jalview_error"),
+ new String[]
+ { sh.getName() }),
+ MessageManager.getString("label.internal_jalview_error"),
JvOptionPane.WARNING_MESSAGE);
return;
if ((wsInfo = setWebService(sh)) == null)
{
- JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
- .formatMessage("label.seq_search_service_is_unknown",
- new String[] { sh.getName() }), MessageManager
- .getString("label.internal_jalview_error"),
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.seq_search_service_is_unknown", new String[]
+ { sh.getName() }),
+ MessageManager.getString("label.internal_jalview_error"),
JvOptionPane.WARNING_MESSAGE);
return;
// sequence db
boolean profileSearch = msa.getSequences().length > 2 ? true : false;
// single sequence or profile from alignment view
- wsInfo.setProgressText("Searching "
- + visdb
- + (!profileSearch ? " with sequence "
- + msa.getSequences()[0].getRefSeq().getName()
- : " with profile") + " from " + altitle
- + "\nJob details\n");
+ wsInfo.setProgressText("Searching " + visdb
+ + (!profileSearch
+ ? " with sequence "
+ + msa.getSequences()[0].getRefSeq().getName()
+ : " with profile")
+ + " from " + altitle + "\nJob details\n");
String jobtitle = WebServiceName
+ ((WebServiceName.indexOf("earch") > -1) ? " " : " search ")
- + " of "
- + visdb
- + (!profileSearch ? " with sequence "
- + msa.getSequences()[0].getRefSeq().getName()
- : " with profile") + " from " + altitle;
+ + " of " + visdb
+ + (!profileSearch
+ ? " with sequence "
+ + msa.getSequences()[0].getRefSeq().getName()
+ : " with profile")
+ + " from " + altitle;
SeqSearchWSThread ssthread = new SeqSearchWSThread(server, WsURL,
wsInfo, alignFrame, WebServiceName, jobtitle, msa, db,
seqdataset);
if (!locateWebService())
{
throw new Exception(MessageManager.formatMessage(
- "exception.cannot_contact_service_endpoint_at",
- new String[] { WsURL }));
+ "exception.cannot_contact_service_endpoint_at", new String[]
+ { WsURL }));
}
String database = server.getDatabase();
if (database == null)
JMenu defmenu = (JMenu) dbsrchs.get("Default Database");
if (defmenu == null)
{
- dbsrchs.put("Default Database", defmenu = new JMenu(
- "Default Database"));
+ dbsrchs.put("Default Database",
+ defmenu = new JMenu("Default Database"));
newdbsrch.addElement(defmenu);
}
{
jalview.bin.Cache.log.warn(
"Database list request failed, so disabling SeqSearch Service client "
- + sh.getName() + " at " + sh.getEndpointURL(), e);
+ + sh.getName() + " at " + sh.getEndpointURL(),
+ e);
return;
}
JMenuItem method;
int nseqs = 0;
if (minlen < 0)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_minlen_must_be_greater_zero"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_minlen_must_be_greater_zero"));
}
for (int i = 0; i < seqs.length; i++)
{
}
boolean valid = nseqs >= 1; // need at least one sequence for valid input
// TODO: generalise
- vamsas.objects.simple.Sequence[] seqarray = (valid) ? new vamsas.objects.simple.Sequence[nseqs]
+ vamsas.objects.simple.Sequence[] seqarray = (valid)
+ ? new vamsas.objects.simple.Sequence[nseqs]
: null;
boolean submitGaps = (nseqs == 1) ? false : true; // profile is submitted
// with gaps
String empty = null;
if (seqs[i].getEnd() >= seqs[i].getStart())
{
- empty = (submitGaps) ? seqs[i].getSequenceAsString() : AlignSeq
- .extractGaps(jalview.util.Comparison.GapChars,
+ empty = (submitGaps) ? seqs[i].getSequenceAsString()
+ : AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
seqs[i].getSequenceAsString());
}
emptySeqs.add(new String[] { newname, empty });
@Override
public boolean hasResults()
{
- if (subjobComplete
- && result != null
- && result.isFinished()
+ if (subjobComplete && result != null && result.isFinished()
&& ((SeqSearchResult) result).getAlignment() != null
- && ((SeqSearchResult) result).getAlignment().getSeqs() != null)
+ && ((SeqSearchResult) result).getAlignment()
+ .getSeqs() != null)
{
return true;
}
// int alseq_l = 0;
if (((SeqSearchResult) result).getAlignment() != null)
{
- alseqs = getVamsasAlignment(((SeqSearchResult) result)
- .getAlignment());
+ alseqs = getVamsasAlignment(
+ ((SeqSearchResult) result).getAlignment());
// alseq_gapchar = ( (SeqSearchResult)
// result).getAlignment().getGapchar().charAt(0);
// alseq_l = alseqs.length;
}
} catch (Exception e)
{
- System.err
- .println("Failed to parse the annotation file associated with the alignment.");
+ System.err.println(
+ "Failed to parse the annotation file associated with the alignment.");
System.err.println(">>>EOF" + inFile + "\n<<<EOF\n");
e.printStackTrace(System.err);
}
inFile = ((SeqSearchResult) result).getFeatures();
if (inFile != null && inFile.length() > 0)
{
- jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(
- inFile, jalview.io.DataSourceType.PASTE);
+ jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(inFile,
+ jalview.io.DataSourceType.PASTE);
ff.parse(al, featureColours, false);
}
} catch (Exception e)
{
- System.err
- .println("Failed to parse the Features file associated with the alignment.");
+ System.err.println(
+ "Failed to parse the Features file associated with the alignment.");
System.err.println(">>>EOF" + inFile + "\n<<<EOF\n");
e.printStackTrace(System.err);
}
}
} catch (Exception e)
{
- System.err
- .println("Failed to parse the treeFile associated with the alignment.");
+ System.err.println(
+ "Failed to parse the treeFile associated with the alignment.");
System.err.println(">>>EOF" + inFile + "\n<<<EOF\n");
e.printStackTrace(System.err);
}
"Exception whilst cancelling " + jobs[job].getJobId(),
exc);
}
- wsInfo.setProgressText(jobs[job].getJobnum(), OutputHeader
- + cancelledMessage + "\n");
+ wsInfo.setProgressText(jobs[job].getJobnum(),
+ OutputHeader + cancelledMessage + "\n");
}
}
if (cancelled)
@Override
public void pollJob(AWsJob job) throws Exception
{
- ((SeqSearchWSJob) job).result = server.getResult(((SeqSearchWSJob) job)
- .getJobId());
+ ((SeqSearchWSJob) job).result = server
+ .getResult(((SeqSearchWSJob) job).getJobId());
}
@Override
if (!(job instanceof SeqSearchWSJob))
{
throw new Error(MessageManager.formatMessage(
- "error.implementation_error_msawbjob_called",
- new String[] { job.getClass().toString() }));
+ "error.implementation_error_msawbjob_called", new String[]
+ { job.getClass().toString() }));
}
SeqSearchWSJob j = (SeqSearchWSJob) job;
if (j.isSubmitted())
{
if (Cache.log.isDebugEnabled())
{
- Cache.log.debug("Tried to submit an already submitted job "
- + j.getJobId());
+ Cache.log.debug(
+ "Tried to submit an already submitted job " + j.getJobId());
}
return;
}
j.setSubmitted(true);
j.result = new MsaResult();
j.result.setFinished(true);
- j.result.setStatus(MessageManager
- .getString("label.empty_alignment_job"));
+ j.result.setStatus(
+ MessageManager.getString("label.empty_alignment_job"));
((MsaResult) j.result).setMsa(null);
}
try
{
- vamsas.objects.simple.WsJobId jobsubmit = server.search(
- j.seqs.getSeqs()[0], dbArg);
+ vamsas.objects.simple.WsJobId jobsubmit = server
+ .search(j.seqs.getSeqs()[0], dbArg);
if ((jobsubmit != null) && (jobsubmit.getStatus() == 1))
{
{
throw new Exception(MessageManager.formatMessage(
"exception.web_service_returned_null_try_later",
- new String[] { WsUrl }));
+ new String[]
+ { WsUrl }));
}
throw new Exception(jobsubmit.getJobId());
{
// TODO: JBPNote catch timeout or other fault types explicitly
// For unexpected errors
- System.err
- .println(WebServiceName
- + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
- + "When contacting Server:" + WsUrl + "\n"
- + e.toString() + "\n");
+ System.err.println(WebServiceName
+ + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
+ + "When contacting Server:" + WsUrl + "\n" + e.toString()
+ + "\n");
j.setAllowedServerExceptions(0);
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
wsInfo.setStatus(j.getJobnum(),
String[] lines = valign.getMethod();
for (int line = 0; line < lines.length; line++)
{
- wsInfo.appendProgressText(jobs[j].getJobnum(), lines[line]
- + "\n");
+ wsInfo.appendProgressText(jobs[j].getJobnum(),
+ lines[line] + "\n");
}
// JBPNote The returned files from a webservice could be
// hidden behind icons in the monitor window that,
} catch (Exception ex)
{
- Cache.log.error("Unexpected exception when processing results for "
- + alTitle, ex);
+ Cache.log.error(
+ "Unexpected exception when processing results for " + alTitle,
+ ex);
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
}
if (results > 0)
* propagateDatasetMappings(al); }
*/
- AlignFrame af = new AlignFrame(al,// columnselection,
+ AlignFrame af = new AlignFrame(al, // columnselection,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
if (nf != null)
{
- af.showNewickTree(nf, MessageManager.formatMessage(
- "label.tree_from", new String[] { this.alTitle }));
+ af.showNewickTree(nf,
+ MessageManager.formatMessage("label.tree_from", new String[]
+ { this.alTitle }));
}
// initialise with same renderer settings as in parent alignframe.
af.getFeatureRenderer().transferSettings(this.featureSettings);
* @author JimP
*
*/
-public abstract class WS1Client extends WSClient implements
- WSMenuEntryProviderI
+public abstract class WS1Client extends WSClient
+ implements WSMenuEntryProviderI
{
/**
{
if (serviceHandle == null)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_cannot_attach_ws_menu_entry"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_cannot_attach_ws_menu_entry"));
}
attachWSMenuEntry(wsmenu, serviceHandle, alignFrame);
}
Map<String, String[]> fmap;
featureMap.put(compbio.ws.client.Services.IUPredWS.toString(),
fmap = new HashMap<String, String[]>());
- fmap.put("Glob", new String[] { "Globular Domain",
- "Predicted globular domain" });
+ fmap.put("Glob",
+ new String[]
+ { "Globular Domain", "Predicted globular domain" });
featureMap.put(compbio.ws.client.Services.JronnWS.toString(),
fmap = new HashMap<String, String[]>());
featureMap.put(compbio.ws.client.Services.DisemblWS.toString(),
fmap.put("COILS", new String[] { "COILS", "Random coil" });
featureMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
fmap = new HashMap<String, String[]>());
- fmap.put("GlobDoms", new String[] { "Globular Domain",
- "Predicted globular domain" });
- fmap.put("Disorder", new String[] { "Protein Disorder",
- "Probable unstructured peptide region" });
+ fmap.put("GlobDoms",
+ new String[]
+ { "Globular Domain", "Predicted globular domain" });
+ fmap.put("Disorder",
+ new String[]
+ { "Protein Disorder", "Probable unstructured peptide region" });
Map<String, Map<String, Object>> amap;
annotMap = new HashMap<String, Map<String, Map<String, Object>>>();
annotMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
{
Cache.log
.info("Couldn't recover disorder prediction for sequence "
- + seq.getName()
- + "(Prediction name was "
- + seqId
+ + seq.getName() + "(Prediction name was " + seqId
+ ")"
+ "\nSee http://issues.jalview.org/browse/JAL-1319 for one possible reason why disorder predictions might fail.");
}
}
if (vals.hasNext())
{
- sf = new SequenceFeature(type[0], type[1],
- base + rn.from, base + rn.to, val = vals.next()
- .floatValue(), methodName);
+ sf = new SequenceFeature(type[0], type[1], base + rn.from,
+ base + rn.to, val = vals.next().floatValue(),
+ methodName);
}
else
{
- sf = new SequenceFeature(type[0], type[1], null, base
- + rn.from, base + rn.to, methodName);
+ sf = new SequenceFeature(type[0], type[1], null,
+ base + rn.from, base + rn.to, methodName);
}
dseq.addSequenceFeature(sf);
if (last != val && !Float.isNaN(last))
typename = service.serviceType + " ("
+ scr.getMethod() + ")",
calcName = service.getServiceTypeURI() + "/"
- + scr.getMethod(), aseq, base + 1, scr);
+ + scr.getMethod(),
+ aseq, base + 1, scr);
annot.graph = AlignmentAnnotation.LINE_GRAPH;
Map<String, Object> styleMap = (annotTypeMap == null) ? null
: annotTypeMap.get(scr.getMethod());
- annot.visible = (styleMap == null || styleMap.get(INVISIBLE) == null);
+ annot.visible = (styleMap == null
+ || styleMap.get(INVISIBLE) == null);
double[] thrsh = (styleMap == null) ? null
: (double[]) styleMap.get(THRESHOLD);
float[] range = (styleMap == null) ? null
annot.description += "<br/>" + threshNote;
}
annot.description += "</html>";
- Color col = ColorUtils.createColourFromName(typeName
- + scr.getMethod());
+ Color col = ColorUtils
+ .createColourFromName(typeName + scr.getMethod());
for (int p = 0, ps = annot.annotations.length; p < ps; p++)
{
if (annot.annotations[p] != null)
((jalview.gui.AlignViewport) alignViewport).setCalcIdSettingsFor(
getCalcId(),
new AAConSettings(true, service, this.preset,
- (arguments != null) ? JabaParamStore
- .getJwsArgsfromJaba(arguments) : null), true);
+ (arguments != null)
+ ? JabaParamStore.getJwsArgsfromJaba(arguments)
+ : null),
+ true);
}
}
super(alignViewport, alignPanel);
}
- public AbstractJabaCalcWorker(Jws2Instance service,
- AlignFrame alignFrame, WsParamSetI preset, List<Argument> paramset)
+ public AbstractJabaCalcWorker(Jws2Instance service, AlignFrame alignFrame,
+ WsParamSetI preset, List<Argument> paramset)
{
this(alignFrame.getCurrentView(), alignFrame.alignPanel);
this.guiProgress = alignFrame;
}
if (collectAnnotationResultsFor(rslt))
{
- jalview.bin.Cache.log
- .debug("Updating result annotation from Job " + rslt
- + " at " + service.getUri());
+ jalview.bin.Cache.log.debug("Updating result annotation from Job "
+ + rslt + " at " + service.getUri());
updateResultAnnotation(true);
ap.adjustAnnotationHeight();
}
catch (JobSubmissionException x)
{
- System.err.println("submission error with " + getServiceActionText()
- + " :");
+ System.err.println(
+ "submission error with " + getServiceActionText() + " :");
x.printStackTrace();
calcMan.disableWorker(this);
} catch (ResultNotAvailableException x)
AnnotatedCollectionI inputSeqs)
{
if (alignment == null || alignment.getWidth() <= 0
- || alignment.getSequences() == null || alignment.isNucleotide() ? !nucleotidesAllowed
- : !proteinAllowed)
+ || alignment.getSequences() == null || alignment.isNucleotide()
+ ? !nucleotidesAllowed
+ : !proteinAllowed)
{
return null;
}
for (SequenceI sq : (inputSeqs.getSequences()))
{
- if (bySequence ? sq.findPosition(end + 1)
- - sq.findPosition(start + 1) > minlen - 1 : sq.getEnd()
- - sq.getStart() > minlen - 1)
+ if (bySequence
+ ? sq.findPosition(end + 1)
+ - sq.findPosition(start + 1) > minlen - 1
+ : sq.getEnd() - sq.getStart() > minlen - 1)
{
String newname = SeqsetUtils.unique_name(seqs.size() + 1);
// make new input sequence with or without gaps
FastaSequence sq = seqs.get(p);
int l = sq.getSequence().length();
// strip gapped columns
- char[] padded = new char[realw], orig = sq.getSequence()
- .toCharArray();
+ char[] padded = new char[realw],
+ orig = sq.getSequence().toCharArray();
for (int i = 0, pp = 0; i < realw; pp++)
{
if (gapMap[pp])
@Override
public boolean isQueued()
{
- return status == null ? false : status.equals(status.SUBMITTED)
- || status.equals(status.PENDING);
+ return status == null ? false
+ : status.equals(status.SUBMITTED)
+ || status.equals(status.PENDING);
}
/*
public boolean isRunning()
{
// TODO Auto-generated method stub
- return status != null
- && (status.equals(status.RUNNING) || status
- .equals(status.STARTED));
+ return status != null && (status.equals(status.RUNNING)
+ || status.equals(status.STARTED));
}
/*
}
else
{
- System.err
- .println("Warning: Ignoring parameter set instance of type "
+ System.err.println(
+ "Warning: Ignoring parameter set instance of type "
+ paramset.getClass()
+ " : Bound but not applicable for service at "
+ service.getUri());
{
throw new Error(MessageManager.formatMessage(
"error.implementation_error_cannot_handle_jaba_param",
- new String[] { rg.getClass().toString() }));
+ new String[]
+ { rg.getClass().toString() }));
}
else
{
List rgs = new ArrayList();
for (ArgumentI rg : jwsargs)
{
- Argument narg = (rg instanceof JabaOption) ? ((JabaOption) rg)
- .getOption() : null;
+ Argument narg = (rg instanceof JabaOption)
+ ? ((JabaOption) rg).getOption()
+ : null;
if (narg == null)
{
throw new Error(MessageManager.formatMessage(
"error.implementation_error_cannot_handle_jaba_param",
- new String[] { rg.getClass().toString() }));
+ new String[]
+ { rg.getClass().toString() }));
}
else
{
@Override
public boolean presetExists(String name)
{
- return (editedParams.containsKey(name) || servicePresets
- .containsKey(name));
+ return (editedParams.containsKey(name)
+ || servicePresets.containsKey(name));
}
@Override
}
if (servicePresets.containsKey(name))
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_attempt_to_delete_service_preset"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_attempt_to_delete_service_preset"));
}
}
public void updatePreset(String oldName, String presetName, String text,
List<ArgumentI> jobParams)
{
- JabaWsParamSet jps = (JabaWsParamSet) ((oldName != null) ? getPreset(oldName)
+ JabaWsParamSet jps = (JabaWsParamSet) ((oldName != null)
+ ? getPreset(oldName)
: getPreset(presetName));
if (jps == null)
{
- throw new Error(
- MessageManager
- .formatMessage(
- "error.implementation_error_cannot_locate_oldname_presetname",
- new String[] { oldName, presetName }));
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_error_cannot_locate_oldname_presetname",
+ new String[]
+ { oldName, presetName }));
}
jps.setName(presetName);
jps.setDescription(text);
{
if (!involves(urls))
{
- throw new IOException(
- MessageManager
- .getString("error.implementation_error_cannot_find_service_url_in_given_set"));
+ throw new IOException(MessageManager.getString(
+ "error.implementation_error_cannot_find_service_url_in_given_set"));
}
JabaWsParamSet wsp = new JabaWsParamSet();
{
lines.add(st.nextToken());
}
- wsp.setjabaArguments(ParameterUtils.processParameters(lines,
- serviceOptions, " "));
+ wsp.setjabaArguments(
+ ParameterUtils.processParameters(lines, serviceOptions, " "));
return wsp;
}
{
if (!involves(pset.getApplicableUrls()))
{
- throw new IOException(
- MessageManager
- .formatMessage(
- "error.implementation_error_cannot_find_service_url_in_given_set_param_store",
- new String[] { service.getUri() }));
+ throw new IOException(MessageManager.formatMessage(
+ "error.implementation_error_cannot_find_service_url_in_given_set_param_store",
+ new String[]
+ { service.getUri() }));
}
if (!(pset instanceof JabaWsParamSet))
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_jabaws_param_set_only_handled_by"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_jabaws_param_set_only_handled_by"));
}
StringBuffer rslt = new StringBuffer();
@Override
public void setSourceFile(String newfile)
{
- throw new Error(MessageManager.formatMessage(
- "error.cannot_set_source_file_for", new String[] { getClass()
- .toString() }));
+ throw new Error(MessageManager
+ .formatMessage("error.cannot_set_source_file_for", new String[]
+ { getClass().toString() }));
}
@Override
{
try
{
- return JabaParamStore.getJwsArgsfromJaba(p.getArguments(service
- .getRunnerConfig()));
+ return JabaParamStore.getJwsArgsfromJaba(
+ p.getArguments(service.getRunnerConfig()));
} catch (Exception e)
{
e.printStackTrace();
- throw new Error(
- MessageManager
- .getString("error.mismatch_service_instance_preset"));
+ throw new Error(MessageManager
+ .getString("error.mismatch_service_instance_preset"));
}
}
@Override
public void setArguments(List<ArgumentI> args)
{
- throw new Error(
- MessageManager
- .getString("error.cannot_set_params_for_ws_preset"));
+ throw new Error(MessageManager
+ .getString("error.cannot_set_params_for_ws_preset"));
}
}
srv_set = registry.getSupportedServices();
// dan test
- System.out.println("registry.getSupportedServices: "
- + srv_set.toString());
+ System.out.println(
+ "registry.getSupportedServices: " + srv_set.toString());
svccategories = registry.getServiceCategories();
rslt = aaservice.customAnalize(seqs, getJabaArguments());
} catch (WrongParameterException x)
{
- throw new JobSubmissionException(
- MessageManager
- .getString("exception.jobsubmission_invalid_params_set"),
- x);
+ throw new JobSubmissionException(MessageManager.getString(
+ "exception.jobsubmission_invalid_params_set"), x);
}
}
import compbio.metadata.ResultNotAvailableException;
import compbio.metadata.WrongParameterException;
-public abstract class JabawsMsaInterfaceAlignCalcWorker extends
- AbstractJabaCalcWorker
+public abstract class JabawsMsaInterfaceAlignCalcWorker
+ extends AbstractJabaCalcWorker
{
@SuppressWarnings("unchecked")
}
public JabawsMsaInterfaceAlignCalcWorker(Jws2Instance service,
- AlignFrame alignFrame, WsParamSetI preset, List<Argument> paramset)
+ AlignFrame alignFrame, WsParamSetI preset,
+ List<Argument> paramset)
{
this(alignFrame.getCurrentView(), alignFrame.alignPanel);
this.guiProgress = alignFrame;
rslt = msaservice.customAlign(seqs, getJabaArguments());
} catch (WrongParameterException x)
{
- throw new JobSubmissionException(
- MessageManager
- .getString("exception.jobsubmission_invalid_params_set"),
- x);
+ throw new JobSubmissionException(MessageManager.getString(
+ "exception.jobsubmission_invalid_params_set"), x);
}
}
return rslt;
this.preset = preset;
if (preset != null)
{
- if (!((preset instanceof JabaPreset) || preset instanceof JabaWsParamSet))
+ if (!((preset instanceof JabaPreset)
+ || preset instanceof JabaWsParamSet))
{
/*
* { this.preset = ((JabaPreset) preset).p; } else if (preset instanceof
* arguments. for (Argument opt : arguments) { newargs.add(opt); } }
* paramset = newargs; } else {
*/
- throw new Error(
- MessageManager
- .getString("error.implementation_error_can_only_instantiate_jaba_param_sets"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_can_only_instantiate_jaba_param_sets"));
}
}
else
sh.paramStore = new JabaParamStore(sh,
Desktop.getUserParameterStore());
}
- WsJobParameters jobParams = (preset == null && paramset != null && paramset
- .size() > 0) ? new WsJobParameters(null, sh, null, paramset)
- : new WsJobParameters(sh, preset);
+ WsJobParameters jobParams = (preset == null && paramset != null
+ && paramset.size() > 0)
+ ? new WsJobParameters(null, sh, null, paramset)
+ : new WsJobParameters(sh, preset);
if (adjustingExisting)
{
jobParams.setName(MessageManager
WsParamSetI prset = jobParams.getPreset();
if (prset == null)
{
- paramset = jobParams.isServiceDefaults() ? null : JabaParamStore
- .getJabafromJwsArgs(jobParams.getJobParams());
+ paramset = jobParams.isServiceDefaults() ? null
+ : JabaParamStore
+ .getJabafromJwsArgs(jobParams.getJobParams());
this.preset = null;
}
else
WsURL = serv.hosturl;
if (!b)
{
- return new WebserviceInfo(WebServiceJobTitle, WebServiceJobTitle
- + " using service hosted at " + serv.hosturl + "\n"
- + (serv.description != null ? serv.description : ""), false);
+ return new WebserviceInfo(WebServiceJobTitle,
+ WebServiceJobTitle + " using service hosted at "
+ + serv.hosturl + "\n"
+ + (serv.description != null ? serv.description : ""),
+ false);
}
return null;
}
removeCurrentAAConWorkerFor(aaui, alignFrame);
buildCurrentAAConWorkerFor(aaui, alignFrame, service);
}
- }// );
+ } // );
}
}
}
final JCheckBoxMenuItem aaConEnabled = new JCheckBoxMenuItem(
aaui.getAAconToggle());
- aaConEnabled.setToolTipText(JvSwingUtils.wrapTooltip(true,
- aaui.getAAconToggleTooltip()));
+ aaConEnabled.setToolTipText(
+ JvSwingUtils.wrapTooltip(true, aaui.getAAconToggleTooltip()));
aaConEnabled.addActionListener(new ActionListener()
{
@Override
});
wsmenu.add(aaConEnabled);
- final JMenuItem modifyParams = new JMenuItem(aaui.getAAeditSettings());
+ final JMenuItem modifyParams = new JMenuItem(
+ aaui.getAAeditSettings());
modifyParams.setToolTipText(JvSwingUtils.wrapTooltip(true,
aaui.getAAeditSettingsTooltip()));
modifyParams.addActionListener(new ActionListener()
public void menuSelected(MenuEvent arg0)
{
// TODO: refactor to the implementing class.
- if (alignFrame.getViewport().getAlignment().isNucleotide() ? aaui
- .isNa() : aaui.isPr())
+ if (alignFrame.getViewport().getAlignment().isNucleotide()
+ ? aaui.isNa()
+ : aaui.isPr())
{
aaConEnabled.setEnabled(true);
modifyParams.setEnabled(true);
{
if (service != null)
{
- if (!service.serviceType.toString().equals(
- compbio.ws.client.Services.AAConWS.toString()))
+ if (!service.serviceType.toString()
+ .equals(compbio.ws.client.Services.AAConWS.toString()))
{
- Cache.log
- .warn("Ignoring invalid preferred service for AACon calculations (service type was "
+ Cache.log.warn(
+ "Ignoring invalid preferred service for AACon calculations (service type was "
+ service.serviceType + ")");
service = null;
}
{
try
{
- Cache.log
- .debug("Waiting around for old discovery thread to finish.");
+ Cache.log.debug(
+ "Waiting around for old discovery thread to finish.");
// wait around until old discoverer dies
Thread.sleep(100);
} catch (Exception e)
// first set up exclusion list if needed
final Set<String> ignoredServices = new HashSet<String>();
- for (String ignored : Cache.getDefault("IGNORED_JABAWS_SERVICETYPES",
- "").split("\\|"))
+ for (String ignored : Cache
+ .getDefault("IGNORED_JABAWS_SERVICETYPES", "").split("\\|"))
{
ignoredServices.add(ignored);
}
oldthread = Thread.currentThread();
try
{
- Class foo = getClass().getClassLoader().loadClass(
- "compbio.ws.client.Jws2Client");
+ Class foo = getClass().getClassLoader()
+ .loadClass("compbio.ws.client.Jws2Client");
} catch (ClassNotFoundException e)
{
- System.err
- .println("Not enabling JABA Webservices : client jar is not available."
+ System.err.println(
+ "Not enabling JABA Webservices : client jar is not available."
+ "\nPlease check that your webstart JNLP file is up to date!");
running = false;
return;
}
if (aborted)
{
- Cache.log.debug("Aborting " + qrys.size()
- + " JABAWS discovery threads.");
+ Cache.log.debug(
+ "Aborting " + qrys.size() + " JABAWS discovery threads.");
for (JabaWsServerQuery squery : qrys)
{
squery.setQuit(true);
}
oldthread = null;
running = false;
- changeSupport.firePropertyChange("services",
- new Vector<Jws2Instance>(), services);
+ changeSupport.firePropertyChange("services", new Vector<Jws2Instance>(),
+ services);
}
/**
{
services = new Vector<Jws2Instance>();
}
- System.out.println("Discovered service: " + jwsservers + " "
- + service.toString());
+ System.out.println(
+ "Discovered service: " + jwsservers + " " + service.toString());
// Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(),
// service2);
service.attachWSMenuEntry(atpoint, alignFrame);
if (alternates.containsKey(service.serviceType))
{
- atpoint.add(hitm = new JMenu(MessageManager
- .getString("label.switch_server")));
+ atpoint.add(hitm = new JMenu(
+ MessageManager.getString("label.switch_server")));
hitm.setToolTipText(JvSwingUtils.wrapTooltip(false,
MessageManager.getString("label.choose_jabaws_server")));
for (final Jws2Instance sv : alternates.get(service.serviceType))
* submenus to index by host and service program type
*/
private void addEnumeratedServices(final JMenu jws2al,
- final AlignFrame alignFrame, List<Jws2Instance> enumerableServices)
+ final AlignFrame alignFrame,
+ List<Jws2Instance> enumerableServices)
{
- boolean byhost = Cache.getDefault("WSMENU_BYHOST", false), bytype = Cache
- .getDefault("WSMENU_BYTYPE", false);
+ boolean byhost = Cache.getDefault("WSMENU_BYHOST", false),
+ bytype = Cache.getDefault("WSMENU_BYTYPE", false);
/**
* eventually, JWS2 services will appear under the same align/etc submenus.
* for moment we keep them separate.
// now add hosts in order of the given array
for (String host : hostlist)
{
- Jws2Instance orderedsvcs[] = hosts.get(host).toArray(
- new Jws2Instance[1]);
+ Jws2Instance orderedsvcs[] = hosts.get(host)
+ .toArray(new Jws2Instance[1]);
String sortbytype[] = new String[orderedsvcs.length];
for (int i = 0; i < sortbytype.length; i++)
{
atpoint = JvSwingUtils.findOrCreateMenu(atpoint, host);
if (atpoint.getToolTipText() == null)
{
- atpoint.setToolTipText(MessageManager.formatMessage(
- "label.services_at", new String[] { host }));
+ atpoint.setToolTipText(MessageManager
+ .formatMessage("label.services_at", new String[]
+ { host }));
}
}
if (bytype)
atpoint.setToolTipText(service.getActionText());
}
}
- if (!byhost
- && !hostLabels.contains(host + service.serviceType
- + service.getActionText()))
+ if (!byhost && !hostLabels.contains(
+ host + service.serviceType + service.getActionText()))
// !hostLabels.contains(host + (bytype ?
// service.serviceType+service.getActionText() : "")))
{
Desktop.showUrl(service.getHost());
}
});
- hitm.setToolTipText(JvSwingUtils.wrapTooltip(true,
- MessageManager.getString("label.open_jabaws_web_page")));
+ hitm.setToolTipText(
+ JvSwingUtils.wrapTooltip(true, MessageManager
+ .getString("label.open_jabaws_web_page")));
lasthostFor.put(service.action, host);
}
- hostLabels.add(host + service.serviceType
- + service.getActionText());
+ hostLabels.add(
+ host + service.serviceType + service.getActionText());
}
service.attachWSMenuEntry(atpoint, alignFrame);
}
;
}
- Thread runner = getDiscoverer().startDiscoverer(
- new PropertyChangeListener()
+ Thread runner = getDiscoverer()
+ .startDiscoverer(new PropertyChangeListener()
{
@Override
for (Jws2Instance instance : getDiscoverer().services)
{
System.out.println("Service " + i++ + " "
- + instance.getClass() + "@"
- + instance.getHost() + ": "
- + instance.getActionText());
+ + instance.getClass() + "@" + instance.getHost()
+ + ": " + instance.getActionText());
}
}
{
Cache.log.warn("Problem whilst trying to make a URL from '"
+ ((url != null) ? url : "<null>") + "'");
- Cache.log
- .warn("This was probably due to a malformed comma separated list"
- + " in the "
- + JWS2HOSTURLS
+ Cache.log.warn(
+ "This was probably due to a malformed comma separated list"
+ + " in the " + JWS2HOSTURLS
+ " entry of $(HOME)/.jalview_properties)");
Cache.log.debug("Exception was ", ex);
}
try
{
compbio.ws.client.WSTester
- .main(new String[] { "-h=" + foo.toString() });
+ .main(new String[]
+ { "-h=" + foo.toString() });
} catch (Exception e)
{
e.printStackTrace();
urlsWithoutServices = new Vector<String>();
}
- if ((invalidServiceUrls == null || !invalidServiceUrls
- .contains(jwsservers))
+ if ((invalidServiceUrls == null
+ || !invalidServiceUrls.contains(jwsservers))
&& !urlsWithoutServices.contains(jwsservers))
{
urlsWithoutServices.add(jwsservers);
if (getUrlsWithoutServices() != null
&& getUrlsWithoutServices().size() > 0)
{
- ermsg.append(MessageManager.getString("warn.urls_no_jaba") + ": \n");
+ ermsg.append(
+ MessageManager.getString("warn.urls_no_jaba") + ": \n");
for (String svcurl : getUrlsWithoutServices())
{
if (list)
public void setPreferredServiceFor(String serviceType,
String serviceAction, Jws2Instance selectedServer)
{
- setPreferredServiceFor(null, serviceType, serviceAction, selectedServer);
+ setPreferredServiceFor(null, serviceType, serviceAction,
+ selectedServer);
}
/**
if (!(sh.service instanceof MsaWS))
{
// redundant at mo - but may change
- JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
- .formatMessage("label.service_called_is_not_msa_service",
- new String[] { sh.serviceType }), MessageManager
- .getString("label.internal_jalview_error"),
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.service_called_is_not_msa_service",
+ new String[]
+ { sh.serviceType }),
+ MessageManager.getString("label.internal_jalview_error"),
JvOptionPane.WARNING_MESSAGE);
return;
if ((wsInfo = setWebService(sh, false)) == null)
{
JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
- .formatMessage("label.msa_service_is_unknown",
- new String[] { sh.serviceType }), MessageManager
- .getString("label.internal_jalview_error"),
+ .formatMessage("label.msa_service_is_unknown", new String[]
+ { sh.serviceType }),
+ MessageManager.getString("label.internal_jalview_error"),
JvOptionPane.WARNING_MESSAGE);
return;
String jobtitle = WebServiceName.toLowerCase();
if (jobtitle.endsWith("alignment"))
{
- if (submitGaps
- && (!jobtitle.endsWith("realignment") || jobtitle
- .indexOf("profile") == -1))
+ if (submitGaps && (!jobtitle.endsWith("realignment")
+ || jobtitle.indexOf("profile") == -1))
{
int pos = jobtitle.indexOf("alignment");
jobtitle = WebServiceName.substring(0, pos) + "re-alignment of "
+ "alignment of " + altitle;
}
- MsaWSThread msathread = new MsaWSThread(server, preset, paramset,
- WsURL, wsInfo, alignFrame, WebServiceName, jobtitle, msa,
- submitGaps, preserveOrder, seqdataset);
+ MsaWSThread msathread = new MsaWSThread(server, preset, paramset, WsURL,
+ wsInfo, alignFrame, WebServiceName, jobtitle, msa, submitGaps,
+ preserveOrder, seqdataset);
if (msathread.hasValidInput())
{
wsInfo.setthisService(msathread);
if (submitGaps == true)
{
action = "Realign ";
- msawsmenu = new JMenu(MessageManager.formatMessage(
- "label.realign_with_params", new String[] { svcname }));
+ msawsmenu = new JMenu(MessageManager
+ .formatMessage("label.realign_with_params", new String[]
+ { svcname }));
msawsmenu.setToolTipText(MessageManager
.getString("label.align_sequences_to_existing_alignment"));
rmsawsmenu.add(msawsmenu);
final boolean withGaps = submitGaps;
JMenuItem method = new JMenuItem(MessageManager.formatMessage(
- "label.calcname_with_default_settings",
- new String[] { calcName }));
- method.setToolTipText(MessageManager
- .formatMessage("label.action_with_default_settings",
- new String[] { action }));
+ "label.calcname_with_default_settings", new String[]
+ { calcName }));
+ method.setToolTipText(MessageManager.formatMessage(
+ "label.action_with_default_settings", new String[]
+ { action }));
method.addActionListener(new ActionListener()
{
if (msa != null)
{
new MsaWSClient(service, alignFrame.getTitle(), msa, withGaps,
- true, alignFrame.getViewport().getAlignment()
- .getDataset(), alignFrame);
+ true,
+ alignFrame.getViewport().getAlignment().getDataset(),
+ alignFrame);
}
}
// arguments
method = new JMenuItem(
MessageManager.getString("label.edit_settings_and_run"));
- method.setToolTipText(MessageManager
- .getString("label.view_and_change_parameters_before_alignment"));
+ method.setToolTipText(MessageManager.getString(
+ "label.view_and_change_parameters_before_alignment"));
method.addActionListener(new ActionListener()
{
AlignmentView msa = alignFrame.gatherSequencesForAlignment();
if (msa != null)
{
- new MsaWSClient(service, null, null, true, alignFrame
- .getTitle(), msa, withGaps, true, alignFrame
- .getViewport().getAlignment().getDataset(),
+ new MsaWSClient(service, null, null, true,
+ alignFrame.getTitle(), msa, withGaps, true,
+ alignFrame.getViewport().getAlignment().getDataset(),
alignFrame);
}
List<WsParamSetI> presets = service.getParamStore().getPresets();
if (presets != null && presets.size() > 0)
{
- JMenu presetlist = new JMenu(
- MessageManager.formatMessage(
- "label.run_with_preset_params",
- new String[] { calcName }));
+ JMenu presetlist = new JMenu(MessageManager.formatMessage(
+ "label.run_with_preset_params", new String[]
+ { calcName }));
final int showToolTipFor = ToolTipManager.sharedInstance()
.getDismissDelay();
@Override
public void mouseEntered(MouseEvent e)
{
- ToolTipManager.sharedInstance().setDismissDelay(
- QUICK_TOOLTIP);
+ ToolTipManager.sharedInstance()
+ .setDismissDelay(QUICK_TOOLTIP);
}
@Override
public void mouseExited(MouseEvent e)
{
- ToolTipManager.sharedInstance().setDismissDelay(
- showToolTipFor);
+ ToolTipManager.sharedInstance()
+ .setDismissDelay(showToolTipFor);
}
});
- String tooltip = JvSwingUtils
- .wrapTooltip(
- true,
- "<strong>"
- + (preset.isModifiable() ? MessageManager
- .getString("label.user_preset")
- : MessageManager
- .getString("label.service_preset"))
- + "</strong><br/>"
- + preset.getDescription());
+ String tooltip = JvSwingUtils.wrapTooltip(true, "<strong>"
+ + (preset.isModifiable()
+ ? MessageManager.getString("label.user_preset")
+ : MessageManager
+ .getString("label.service_preset"))
+ + "</strong><br/>" + preset.getDescription());
methodR.setToolTipText(tooltip);
methodR.addActionListener(new ActionListener()
{
MsaWSClient msac = new MsaWSClient(service, preset,
alignFrame.getTitle(), msa, false, true,
alignFrame.getViewport().getAlignment()
- .getDataset(), alignFrame);
+ .getDataset(),
+ alignFrame);
}
}
int nseqs = 0;
if (minlen < 0)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_minlen_must_be_greater_zero"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_minlen_must_be_greater_zero"));
}
for (int i = 0; i < seqs.length; i++)
{
String empty = null;
if (seqs[i].getEnd() >= seqs[i].getStart())
{
- empty = (submitGaps) ? seqs[i].getSequenceAsString() : AlignSeq
- .extractGaps(jalview.util.Comparison.GapChars,
+ empty = (submitGaps) ? seqs[i].getSequenceAsString()
+ : AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
seqs[i].getSequenceAsString());
}
emptySeqs.add(new String[] { newname, empty });
@Override
public boolean hasResults()
{
- if (subjobComplete
- && isFinished()
- && (alignment != null || (emptySeqs != null && emptySeqs
- .size() > 0)))
+ if (subjobComplete && isFinished() && (alignment != null
+ || (emptySeqs != null && emptySeqs.size() > 0)))
{
return true;
}
for (compbio.data.sequence.FastaSequence seq : alignment
.getSequences())
{
- alseqs[alseq_l++] = new Sequence(seq.getId(), seq.getSequence());
+ alseqs[alseq_l++] = new Sequence(seq.getId(),
+ seq.getSequence());
}
alseq_gapchar = alignment.getMetadata().getGapchar();
{
for (Argument opt : ((JabaWsParamSet) preset).getjabaArguments())
{
- jobProgress.append(opt.getName() + " " + opt.getDefaultValue()
- + "\n");
+ jobProgress.append(
+ opt.getName() + " " + opt.getDefaultValue() + "\n");
}
}
}
// merge arguments with preset's own arguments.
for (Argument opt : arguments)
{
- jobProgress.append(opt.getName() + " " + opt.getDefaultValue()
- + "\n");
+ jobProgress.append(
+ opt.getName() + " " + opt.getDefaultValue() + "\n");
}
}
jobProgress.append("\nJob Output:\n");
"Exception whilst cancelling " + jobs[job].getJobId(),
exc);
}
- wsInfo.setProgressText(jobs[job].getJobnum(), OutputHeader
- + cancelledMessage + "\n");
+ wsInfo.setProgressText(jobs[job].getJobnum(),
+ OutputHeader + cancelledMessage + "\n");
}
else
{
do
{
j.setLastChunk(lastchunk);
- ChunkHolder chunk = server
- .pullExecStatistics(j.getJobId(), lastchunk);
+ ChunkHolder chunk = server.pullExecStatistics(j.getJobId(),
+ lastchunk);
if (chunk != null)
{
changed |= chunk.getChunk().length() > 0;
if (!(job instanceof MsaWSJob))
{
throw new Error(MessageManager.formatMessage(
- "error.implementation_error_msawbjob_called",
- new String[] { job.getClass().toString() }));
+ "error.implementation_error_msawbjob_called", new String[]
+ { job.getClass().toString() }));
}
MsaWSJob j = (MsaWSJob) job;
if (j.isSubmitted())
{
if (Cache.log.isDebugEnabled())
{
- Cache.log.debug("Tried to submit an already submitted job "
- + j.getJobId());
+ Cache.log.debug(
+ "Tried to submit an already submitted job " + j.getJobId());
}
return;
}
{
throw new Exception(MessageManager.formatMessage(
"exception.web_service_returned_null_try_later",
- new String[] { WsUrl }));
+ new String[]
+ { WsUrl }));
}
} catch (compbio.metadata.UnsupportedRuntimeException _lex)
{
lex = _lex;
wsInfo.appendProgressText(MessageManager.formatMessage(
"info.job_couldnt_be_run_server_doesnt_support_program",
- new String[] { _lex.getMessage() }));
+ new String[]
+ { _lex.getMessage() }));
wsInfo.warnUser(_lex.getMessage(),
MessageManager.getString("warn.service_not_supported"));
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
{
lex = _lex;
wsInfo.appendProgressText(MessageManager.formatMessage(
- "info.job_couldnt_be_run_exceeded_hard_limit",
- new String[] { _lex.getMessage() }));
+ "info.job_couldnt_be_run_exceeded_hard_limit", new String[]
+ { _lex.getMessage() }));
wsInfo.warnUser(_lex.getMessage(),
MessageManager.getString("warn.input_is_too_big"));
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
MessageManager.getString("warn.invalid_job_param_set"));
wsInfo.appendProgressText(MessageManager.formatMessage(
"info.job_couldnt_be_run_incorrect_param_setting",
- new String[] { _lex.getMessage() }));
+ new String[]
+ { _lex.getMessage() }));
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
} catch (Error e)
{
// For unexpected errors
- System.err
- .println(WebServiceName
- + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
- + "When contacting Server:" + WsUrl + "\n");
+ System.err.println(WebServiceName
+ + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
+ + "When contacting Server:" + WsUrl + "\n");
e.printStackTrace(System.err);
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
wsInfo.setStatus(j.getJobnum(),
} catch (Exception e)
{
// For unexpected errors
- System.err
- .println(WebServiceName
- + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
- + "When contacting Server:" + WsUrl + "\n");
+ System.err.println(WebServiceName
+ + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
+ + "When contacting Server:" + WsUrl + "\n");
e.printStackTrace(System.err);
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
wsInfo.setStatus(j.getJobnum(),
// TODO: JBPNote catch timeout or other fault types explicitly
j.setAllowedServerExceptions(0);
- wsInfo.appendProgressText(j.getJobnum(), MessageManager
- .getString("info.failed_to_submit_sequences_for_alignment"));
+ wsInfo.appendProgressText(j.getJobnum(), MessageManager.getString(
+ "info.failed_to_submit_sequences_for_alignment"));
}
}
}
} catch (Exception e)
{
- Cache.log
- .warn("Exception when retrieving remaining Job progress data for job "
+ Cache.log.warn(
+ "Exception when retrieving remaining Job progress data for job "
+ msjob.getJobId() + " on server " + WsUrl);
e.printStackTrace();
nexcept--;
{
// job has failed for some reason - probably due to invalid
// parameters
- Cache.log
- .debug("Results not available for finished job - marking as broken job.",
- e);
- msjob.jobProgress
- .append("\nResult not available. Probably due to invalid input or parameter settings. Server error message below:\n\n"
+ Cache.log.debug(
+ "Results not available for finished job - marking as broken job.",
+ e);
+ msjob.jobProgress.append(
+ "\nResult not available. Probably due to invalid input or parameter settings. Server error message below:\n\n"
+ e.getLocalizedMessage());
msjob.setjobStatus(JobStatus.FAILED);
} catch (Exception e)
// wsInfo.appendProgressText(jobs[j].getJobnum(),
// "\nAlignment Object Method Notes\n");
// wsInfo.appendProgressText(jobs[j].getJobnum(),
- // "Calculated with "+alignment.getMetadata().getProgram().toString());
+ // "Calculated with
+ // "+alignment.getMetadata().getProgram().toString());
// JBPNote The returned files from a webservice could be
// hidden behind icons in the monitor window that,
// when clicked, pop up their corresponding data
} catch (Exception ex)
{
- Cache.log.error("Unexpected exception when processing results for "
- + alTitle, ex);
+ Cache.log.error(
+ "Unexpected exception when processing results for " + alTitle,
+ ex);
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
}
if (results > 0)
protected void displayInNewFrame(AlignmentI al,
List<AlignmentOrder> alorders, HiddenColumns hidden)
{
- AlignFrame af = new AlignFrame(al, hidden,
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ AlignFrame af = new AlignFrame(al, hidden, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
// initialise with same renderer settings as in parent alignframe.
af.getFeatureRenderer().transferSettings(this.featureSettings);
* SplitFrame with the other pane similarly aligned.
*/
AlignFrame requestedBy = getRequestingAlignFrame();
- if (requestedBy != null
- && requestedBy.getSplitViewContainer() != null
- && requestedBy.getSplitViewContainer().getComplement(
- requestedBy) != null)
+ if (requestedBy != null && requestedBy.getSplitViewContainer() != null
+ && requestedBy.getSplitViewContainer()
+ .getComplement(requestedBy) != null)
{
AlignmentI complement = requestedBy.getSplitViewContainer()
.getComplement(requestedBy);
af2.setTitle(complementTitle);
String linkedTitle = MessageManager
.getString("label.linked_view_title");
- JInternalFrame splitFrame = new SplitFrame(al.isNucleotide() ? af
- : af2, al.isNucleotide() ? af2 : af);
+ JInternalFrame splitFrame = new SplitFrame(
+ al.isNucleotide() ? af : af2, al.isNucleotide() ? af2 : af);
Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
return;
}
}
for (int i = 0, l = alorders.size(); i < l; i++)
{
- af.addSortByOrderMenuItem(WebServiceName + (names.get(i))
- + " Ordering", alorders.get(i));
+ af.addSortByOrderMenuItem(
+ WebServiceName + (names.get(i)) + " Ordering",
+ alorders.get(i));
}
}
}
{
try
{
- o.setDefaultValue(isParameter(param, pseparator) ? getParamValue(
- param, pseparator) : param);
+ o.setDefaultValue(isParameter(param, pseparator)
+ ? getParamValue(param, pseparator)
+ : param);
} catch (WrongParameterException e)
{
- System.out.println("Problem setting value for the parameter: "
- + param);
+ System.out.println(
+ "Problem setting value for the parameter: " + param);
e.printStackTrace();
}
}
} catch (Exception e)
{
e.printStackTrace();
- throw new Error(
- MessageManager
- .getString("error.implementation_error_couldnt_copy_value_constraint"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_couldnt_copy_value_constraint"));
}
}
descriptionData = data;
}
- String[] typenameAndDescription = constructTypenameAndDescription(descriptionData
- .first());
+ String[] typenameAndDescription = constructTypenameAndDescription(
+ descriptionData.first());
String typename = typenameAndDescription[0];
String description = typenameAndDescription[1];
}
private AlignmentAnnotation constructAnnotationFromScoreHolder(
- AlignmentAnnotation annotation, String struct, TreeSet<Score> data)
+ AlignmentAnnotation annotation, String struct,
+ TreeSet<Score> data)
{
Annotation[] anns = new Annotation[gapMap != null ? gapMap.length + 1
: struct.length()];
- if (data != null
- && data.size() > 1
- && data.first().getMethod()
- .equals(AlifoldResult.contactProbabilities.toString()))
+ if (data != null && data.size() > 1 && data.first().getMethod()
+ .equals(AlifoldResult.contactProbabilities.toString()))
{
// The base pair probabilities are stored in a set in scoreholder. we want
{
// The Score objects contain a set of size one containing the range and
// an ArrayList<float> of size one containing the probabilty
- basePairs.put(score.getRanges().first(), new Float(score
- .getScores().get(0)));
+ basePairs.put(score.getRanges().first(),
+ new Float(score.getScores().get(0)));
}
for (int i = 0, ri = 0, iEnd = struct.length(); i < iEnd; i++, ri++)
description = MessageFormat.format(
"Minimum Free Energy Structure. Energy: {0} = {1} + {2}",
- score.getScores().get(0), score.getScores().get(1), score
- .getScores().get(2));
+ score.getScores().get(0), score.getScores().get(1),
+ score.getScores().get(2));
typename = "MFE Structure";
}
- else if (datatype.equals(AlifoldResult.contactProbabilityStructure
- .toString()))
+ else if (datatype
+ .equals(AlifoldResult.contactProbabilityStructure.toString()))
{
- description = MessageFormat
- .format("Base Pair Contact Probabilities. "
- + "Energy of Ensemble: {0} Frequency of Ensemble: {1}",
- score.getScores().get(0), score.getScores().get(1));
+ description = MessageFormat.format("Base Pair Contact Probabilities. "
+ + "Energy of Ensemble: {0} Frequency of Ensemble: {1}",
+ score.getScores().get(0), score.getScores().get(1));
typename = "Contact Probabilities";
}
else if (datatype.equals(AlifoldResult.centroidStructure.toString()))
{
description = MessageFormat.format(
- "Centroid Structure. Energy: {0} = {1} + {2}", score
- .getScores().get(0), score.getScores().get(1), score
- .getScores().get(2));
+ "Centroid Structure. Energy: {0} = {1} + {2}",
+ score.getScores().get(0), score.getScores().get(1),
+ score.getScores().get(2));
typename = "Centroid Structure";
}
else if (datatype.equals(AlifoldResult.stochBTStructure.toString()))
else if (datatype.equals(AlifoldResult.MEAStucture.toString()))
{
description = MessageFormat.format(
- "Maximum Expected Accuracy Values: '{' {0} MEA={1} '}", score
- .getScores().get(0), score.getScores().get(1));
+ "Maximum Expected Accuracy Values: '{' {0} MEA={1} '}",
+ score.getScores().get(0), score.getScores().get(1));
typename = "MEA Structure";
}
else if (datatype.equals(AlifoldResult.consensusAlignment.toString()))
try
{
worker = (AbstractJabaCalcWorker) (clientClass
- .getConstructor(new Class[] { Jws2Instance.class,
- AlignFrame.class, WsParamSetI.class, List.class })
- .newInstance(new Object[] { sh, alignFrame, this.preset,
- paramset }));
+ .getConstructor(new Class[]
+ { Jws2Instance.class, AlignFrame.class, WsParamSetI.class,
+ List.class })
+ .newInstance(new Object[]
+ { sh, alignFrame, this.preset, paramset }));
} catch (Exception x)
{
x.printStackTrace();
throw new Error(
- MessageManager.getString("error.implementation_error"), x);
+ MessageManager.getString("error.implementation_error"),
+ x);
}
alignFrame.getViewport().getCalcManager().registerWorker(worker);
alignFrame.getViewport().getCalcManager().startWorker(worker);
return;
}
- alignFrame
- .getViewport()
- .getCalcManager()
- .startWorker(
- new AADisorderClient(sh, alignFrame, preset, paramset));
+ alignFrame.getViewport().getCalcManager().startWorker(
+ new AADisorderClient(sh, alignFrame, preset, paramset));
}
}
service.serviceType.length() - 2);
JMenuItem annotservice = new JMenuItem(MessageManager.formatMessage(
- "label.calcname_with_default_settings",
- new String[] { calcName }));
+ "label.calcname_with_default_settings", new String[]
+ { calcName }));
annotservice.addActionListener(new ActionListener()
{
// arguments
annotservice = new JMenuItem(
MessageManager.getString("label.edit_settings_and_run"));
- annotservice
- .setToolTipText(MessageManager
- .getString("label.view_and_change_parameters_before_running_calculation"));
+ annotservice.setToolTipText(MessageManager.getString(
+ "label.view_and_change_parameters_before_running_calculation"));
annotservice.addActionListener(new ActionListener()
{
List<WsParamSetI> presets = service.getParamStore().getPresets();
if (presets != null && presets.size() > 0)
{
- JMenu presetlist = new JMenu(MessageManager.formatMessage(
- "label.run_with_preset", new String[] { calcName }));
+ JMenu presetlist = new JMenu(MessageManager
+ .formatMessage("label.run_with_preset", new String[]
+ { calcName }));
for (final WsParamSetI preset : presets)
{
final JMenuItem methodR = new JMenuItem(preset.getName());
- methodR.setToolTipText(JvSwingUtils.wrapTooltip(
- true,
- "<strong>"
- + (preset.isModifiable() ? MessageManager
- .getString("label.user_preset")
- : MessageManager
- .getString("label.service_preset"))
- + "</strong><br/>" + preset.getDescription()));
+ methodR.setToolTipText(JvSwingUtils.wrapTooltip(true, "<strong>"
+ + (preset.isModifiable()
+ ? MessageManager.getString("label.user_preset")
+ : MessageManager
+ .getString("label.service_preset"))
+ + "</strong><br/>" + preset.getDescription()));
methodR.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
Desktop.instance.showUrl(service.docUrl);
}
});
- annotservice.setToolTipText(JvSwingUtils.wrapTooltip(true,
- MessageManager.formatMessage("label.view_service_doc_url",
- new String[] { service.docUrl, service.docUrl })));
+ annotservice.setToolTipText(
+ JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage(
+ "label.view_service_doc_url", new String[]
+ { service.docUrl, service.docUrl })));
wsmenu.add(annotservice);
}
}
preset = pr;
return;
}
- List<ArgumentI> oldargs = new ArrayList<ArgumentI>(), newargs = new ArrayList<ArgumentI>();
+ List<ArgumentI> oldargs = new ArrayList<ArgumentI>(),
+ newargs = new ArrayList<ArgumentI>();
oldargs.addAll(preset.getArguments());
// need to compare parameters
for (ArgumentI newparg : pr.getArguments())
return;
}
// Try even harder to migrate arguments.
- throw new Error(
- MessageManager
- .getString("error.parameter_migration_not_implemented_yet"));
+ throw new Error(MessageManager
+ .getString("error.parameter_migration_not_implemented_yet"));
}
}
public List<Argument> getJobArgset()
{
- return jobArgset == null ? null : JabaParamStore
- .getJabafromJwsArgs(jobArgset);
+ return jobArgset == null ? null
+ : JabaParamStore.getJabafromJwsArgs(jobArgset);
}
public void setJobArgset(List<Argument> jobArgset)
{
// TODO: test if parameters valid for service
- this.jobArgset = jobArgset == null ? null : JabaParamStore
- .getJwsArgsfromJaba(jobArgset);
+ this.jobArgset = jobArgset == null ? null
+ : JabaParamStore.getJwsArgsfromJaba(jobArgset);
}
public String getWsParamFile()
} catch (Exception e)
{
e.printStackTrace();
- throw new Error(
- MessageManager
- .getString("error.implementation_error_cannot_set_jaba_option"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_cannot_set_jaba_option"));
}
}
{
return ValueType.Integer;
}
- throw new Error(
- MessageManager
- .formatMessage(
- "error.implementation_error_valuetype_doesnt_support_jabaws_type",
- new String[] { vc.toString() }));
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_error_valuetype_doesnt_support_jabaws_type",
+ new String[]
+ { vc.toString() }));
}
@Override
{
if (!allJaba(jobParams))
{
- throw new Error(
- MessageManager
- .getString("error.cannot_create_jabaws_param_set"));
+ throw new Error(MessageManager
+ .getString("error.cannot_create_jabaws_param_set"));
}
else
{
{
if (!allJaba(args))
{
- throw new Error(
- MessageManager
- .getString("error.cannot_set_arguments_to_jabaws_param_set"));
+ throw new Error(MessageManager
+ .getString("error.cannot_set_arguments_to_jabaws_param_set"));
}
jabaArguments = new ArrayList<Option>();
for (ArgumentI rg : args)
}
throw new Error(MessageManager.formatMessage(
"error.implementation_error_runner_config_not_available",
- new String[] { serviceType, service.getClass().toString() }));
+ new String[]
+ { serviceType, service.getClass().toString() }));
}
@Override
// this is only valid for Jaba 1.0 - this formula might have to change!
return hosturl
+ (hosturl.lastIndexOf("/") == (hosturl.length() - 1) ? ""
- : "/") + serviceType;
+ : "/")
+ + serviceType;
}
private boolean hasParams = false, lookedForParams = false;
private static String category_rewrite(String cat_name)
{
- return (cat_name != null && cat_name.equals("Prediction")) ? "Secondary Structure Prediction"
+ return (cat_name != null && cat_name.equals("Prediction"))
+ ? "Secondary Structure Prediction"
: cat_name;
}
* @param hosturl
* @param jabaParamStore
*/
- public void registerParser(String hosturl, ParamDatastoreI paramdataStore);
+ public void registerParser(String hosturl,
+ ParamDatastoreI paramdataStore);
}
{
super(name, descr, required, (defVal ? name : ""), (val ? name : ""),
- Arrays.asList(new String[] { name }), link);
+ Arrays.asList(new String[]
+ { name }), link);
}
}
min = parm.min;
}
- public IntegerParameter(String name, String description,
- boolean required, int defValue, int min, int max)
+ public IntegerParameter(String name, String description, boolean required,
+ int defValue, int min, int max)
{
- super(name, description, required, String.valueOf(defValue), null,
- null, null);
+ super(name, description, required, String.valueOf(defValue), null, null,
+ null);
defval = defValue;
this.min = min;
this.max = max;
}
- public IntegerParameter(String name, String description,
- boolean required, int defValue, int value, int min, int max)
+ public IntegerParameter(String name, String description, boolean required,
+ int defValue, int value, int min, int max)
{
- super(name, description, required, String.valueOf(defValue), String
- .valueOf(value), null, null);
+ super(name, description, required, String.valueOf(defValue),
+ String.valueOf(value), null, null);
defval = defValue;
this.min = min;
this.max = max;
import jalview.ws.params.ParameterI;
import jalview.ws.params.ValueConstrainI;
-public abstract class Parameter extends Option implements OptionI,
- ParameterI
+public abstract class Parameter extends Option
+ implements OptionI, ParameterI
{
ValueConstrainI validator;
if (en == null)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_need_to_have_httpresponse"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_need_to_have_httpresponse"));
}
jalview.io.packed.JalviewDataset ds = restJob.newJalviewDataset();
// Decide how we deal with content.
if (!(en instanceof MultipartEntity))
{
// assume content is simple text stream that can be read from
- String enc = (en.getContentEncoding() == null) ? null : en
- .getContentEncoding().getValue();
+ String enc = (en.getContentEncoding() == null) ? null
+ : en.getContentEncoding().getValue();
if (en.getContentType() != null)
{
Cache.log.debug("Result Type: " + en.getContentType().toString());
{
if (type == null)
{
- return new StringBody(utf8.encode(content).asCharBuffer()
- .toString());
+ return new StringBody(
+ utf8.encode(content).asCharBuffer().toString());
}
else
{
- return new StringBody(utf8.encode(content).asCharBuffer()
- .toString(), type, utf8);
+ return new StringBody(
+ utf8.encode(content).asCharBuffer().toString(), type, utf8);
}
} catch (Exception ex)
{
{
// TODO: revise architecture - this is counter intuitive - options with
// different values to their names are actually parameters
- rg = (arg.getValue().length() > 0) ? (arg.getValue().equals(
- arg.getName()) ? arg.getName() : arg.getName() + "='"
- + arg.getValue() + "'") : arg.getName();
+ rg = (arg.getValue().length() > 0)
+ ? (arg.getValue().equals(arg.getName()) ? arg.getName()
+ : arg.getName() + "='" + arg.getValue() + "'")
+ : arg.getName();
}
if (rg.length() > 0)
{
}
}
StringBuffer warnings;
- if (!configureFromURLtokenString(urltoks, warnings = new StringBuffer()))
+ if (!configureFromURLtokenString(urltoks,
+ warnings = new StringBuffer()))
{
throw new InvalidArgumentException(warnings.toString());
}
protected OptionI createMolTypeOption(String name, String descr,
boolean req, molType curType, molType defType)
{
- return new Option(name, descr, req, defType == null ? ""
- : defType.toString(),
+ return new Option(name, descr, req,
+ defType == null ? "" : defType.toString(),
curType == null ? "" : curType.toString(),
molType.toStringValues(), null);
}
* @author JimP
*
*/
-public class RestClient extends WSClient implements WSClientI,
- WSMenuEntryProviderI
+public class RestClient extends WSClient
+ implements WSClientI, WSMenuEntryProviderI
{
RestServiceDescription service;
public void setWebserviceInfo(boolean headless)
{
- WebServiceJobTitle = MessageManager.formatMessage(
- "label.webservice_job_title", new String[] {
- service.details.Action, service.details.Name });
+ WebServiceJobTitle = MessageManager
+ .formatMessage("label.webservice_job_title", new String[]
+ { service.details.Action, service.details.Name });
WebServiceName = service.details.Name;
WebServiceReference = "No reference - go to url for more info";
if (service.details.description != null)
}
if (!headless)
{
- wsInfo = new WebserviceInfo(WebServiceJobTitle, WebServiceName + "\n"
- + WebServiceReference, true);
+ wsInfo = new WebserviceInfo(WebServiceJobTitle,
+ WebServiceName + "\n" + WebServiceReference, true);
wsInfo.setRenderAsHtml(true);
}
final AlignFrame alignFrame)
{
JMenuItem submit = new JMenuItem(service.details.Name);
- submit.setToolTipText(MessageManager.formatMessage(
- "label.rest_client_submit", new String[] {
- service.details.Action, service.details.Name }));
+ submit.setToolTipText(MessageManager
+ .formatMessage("label.rest_client_submit", new String[]
+ { service.details.Action, service.details.Name }));
submit.addActionListener(new ActionListener()
{
{
// intersect groups with selected region
_input = new AlignmentView(av.getAlignment(),
- av.getAlignment()
- .getHiddenColumns(), av.getSelectionGroup(),
- av.hasHiddenColumns(), true, true);
+ av.getAlignment().getHiddenColumns(),
+ av.getSelectionGroup(), av.hasHiddenColumns(), true,
+ true);
viewTitle = MessageManager.formatMessage(
- "label.select_visible_region_of",
- new String[] {
- (av.hasHiddenColumns() ? MessageManager
- .getString("label.visible") : ""),
+ "label.select_visible_region_of", new String[]
+ { (av.hasHiddenColumns()
+ ? MessageManager.getString("label.visible")
+ : ""),
af.getTitle() });
}
else
{
// use selected region to partition alignment
_input = new AlignmentView(av.getAlignment(),
- av.getAlignment()
- .getHiddenColumns(), av.getSelectionGroup(),
- av.hasHiddenColumns(), false, true);
+ av.getAlignment().getHiddenColumns(),
+ av.getSelectionGroup(), av.hasHiddenColumns(), false,
+ true);
}
viewTitle = MessageManager.formatMessage(
- "label.select_unselect_visible_regions_from",
- new String[] {
- (av.hasHiddenColumns() ? MessageManager
- .getString("label.visible") : ""),
+ "label.select_unselect_visible_regions_from", new String[]
+ { (av.hasHiddenColumns()
+ ? MessageManager.getString("label.visible")
+ : ""),
af.getTitle() });
}
else
{
// just take selected region intersection
_input = new AlignmentView(av.getAlignment(),
- av.getAlignment()
- .getHiddenColumns(), av.getSelectionGroup(),
- av.hasHiddenColumns(), true, true);
+ av.getAlignment().getHiddenColumns(),
+ av.getSelectionGroup(), av.hasHiddenColumns(), true, true);
viewTitle = MessageManager.formatMessage(
- "label.select_visible_region_of",
- new String[] {
- (av.hasHiddenColumns() ? MessageManager
- .getString("label.visible") : ""),
+ "label.select_visible_region_of", new String[]
+ { (av.hasHiddenColumns()
+ ? MessageManager.getString("label.visible")
+ : ""),
af.getTitle() });
}
}
{
// standard alignment view without selection present
_input = new AlignmentView(av.getAlignment(),
- av.getAlignment()
- .getHiddenColumns(), null, av.hasHiddenColumns(), false,
- true);
+ av.getAlignment().getHiddenColumns(), null,
+ av.hasHiddenColumns(), false, true);
viewTitle = ""
- + (av.hasHiddenColumns() ? (new StringBuffer(" ")
- .append(MessageManager
- .getString("label.visible_region_of"))
- .toString()) : "") + af.getTitle();
+ + (av.hasHiddenColumns()
+ ? (new StringBuffer(" ")
+ .append(MessageManager
+ .getString("label.visible_region_of"))
+ .toString())
+ : "")
+ + af.getTitle();
}
RestJobThread jobsthread = new RestJobThread(this);
else
{
// TODO: try to tell the user why the job couldn't be started.
- JvOptionPane
- .showMessageDialog(
- Desktop.desktop,
- (jobsthread.hasWarnings() ? jobsthread.getWarnings()
- : MessageManager
- .getString("label.job_couldnt_be_started_check_input")),
- MessageManager
- .getString("label.unable_start_web_service_analysis"),
- JvOptionPane.WARNING_MESSAGE);
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ (jobsthread.hasWarnings() ? jobsthread.getWarnings()
+ : MessageManager.getString(
+ "label.job_couldnt_be_started_check_input")),
+ MessageManager
+ .getString("label.unable_start_web_service_analysis"),
+ JvOptionPane.WARNING_MESSAGE);
}
}
public static RestClient makeShmmrRestClient()
{
- String action = "Analysis", description = "Sequence Harmony and Multi-Relief (Brandt et al. 2010)", name = MessageManager
- .getString("label.multiharmony");
+ String action = "Analysis",
+ description = "Sequence Harmony and Multi-Relief (Brandt et al. 2010)",
+ name = MessageManager.getString("label.multiharmony");
Hashtable<String, InputType> iparams = new Hashtable<String, InputType>();
jalview.ws.rest.params.JobConstant toolp;
// toolp = new jalview.ws.rest.JobConstant("tool","jalview");
iparams.put("groups", sgroups);
sgroups.token = "groups";
sgroups.sep = " ";
- RestServiceDescription shmrService = new RestServiceDescription(
- action,
- description,
- name,
- "http://zeus.few.vu.nl/programs/shmrwww/index.php?tool=jalview",// ?tool=jalview&mbjob[method]=shmr&mbjob[description]=step1",
+ RestServiceDescription shmrService = new RestServiceDescription(action,
+ description, name,
+ "http://zeus.few.vu.nl/programs/shmrwww/index.php?tool=jalview", // ?tool=jalview&mbjob[method]=shmr&mbjob[description]=step1",
"?tool=jalview", iparams, true, false, '-');
// a priori knowledge of the data returned from the service
shmrService.addResultDatatype(JvDataType.ANNOTATION);
try
{
for (RestServiceDescription descr : RestServiceDescription
- .parseDescriptions(jalview.bin.Cache.getDefault(
- RSBS_SERVICES,
- makeShmmrRestClient().service.toString())))
+ .parseDescriptions(
+ jalview.bin.Cache.getDefault(RSBS_SERVICES,
+ makeShmmrRestClient().service.toString())))
{
services.add(descr.toString());
}
} catch (Exception ex)
{
- System.err
- .println("Serious - RSBS descriptions in user preferences are corrupt!");
+ System.err.println(
+ "Serious - RSBS descriptions in user preferences are corrupt!");
ex.printStackTrace();
}
* @param viscontigs
* visible contigs of an alignment view from which _input was derived
*/
- public RestJob(int jobNum, RestJobThread restJobThread,
- AlignmentI _input, int[] viscontigs)
+ public RestJob(int jobNum, RestJobThread restJobThread, AlignmentI _input,
+ int[] viscontigs)
{
rsd = restJobThread.restClient.service;
jobnum = jobNum;
// get sequences for the alignmentI
// get groups trimmed to alignment columns
// get any annotation trimmed to start/end columns, too.
- squniq = jalview.analysis.SeqsetUtils.uniquify(
- _input.getSequencesArray(), true);
+ squniq = jalview.analysis.SeqsetUtils
+ .uniquify(_input.getSequencesArray(), true);
// prepare input
// form alignment+groups+annotation,preprocess and then record references
// for formatters
}
else
{
- statMessage = ("Not enough groups defined on the alignment - need at least " + prm
- .getValue().min);
+ statMessage = ("Not enough groups defined on the alignment - need at least "
+ + prm.getValue().min);
}
}
}
{
jobs = new RestJob[1];
jobs[0] = new RestJob(0, this,
- restClient._input.getVisibleAlignment(restClient.service
- .getGapCharacter()),
+ restClient._input.getVisibleAlignment(
+ restClient.service.getGapCharacter()),
restClient._input.getVisibleContigs());
// need a function to get a range on a view/alignment and return both
// annotation, groups and selection subsetted to just that region.
{
int[] viscontig = restClient._input.getVisibleContigs();
AlignmentI[] viscontigals = restClient._input
- .getVisibleContigAlignments(restClient.service
- .getGapCharacter());
+ .getVisibleContigAlignments(
+ restClient.service.getGapCharacter());
if (viscontigals != null && viscontigals.length > 0)
{
jobs = new RestJob[viscontigals.length];
{
if (input.getValue().validFor(rj))
{
- postentity.addPart(input.getKey(), input.getValue()
- .formatForInput(rj));
+ postentity.addPart(input.getKey(),
+ input.getValue().formatForInput(rj));
}
else
{
break;
case 202:
rj.statMessage = "<br>Job submitted successfully. Results available at this URL:\n"
- + "<a href="
- + rj.getJobId()
- + "\">"
- + rj.getJobId()
+ + "<a href=" + rj.getJobId() + "\">" + rj.getJobId()
+ "</a><br>";
rj.running = true;
break;
{
if (loc.length > 1)
{
- Cache.log
- .warn("Ignoring additional "
- + (loc.length - 1)
- + " location(s) provided in response header ( next one is '"
- + loc[1].getValue() + "' )");
+ Cache.log.warn("Ignoring additional " + (loc.length - 1)
+ + " location(s) provided in response header ( next one is '"
+ + loc[1].getValue() + "' )");
}
rj.setJobId(loc[0].getValue());
rj.setSubmitted(true);
rj.setSubjobComplete(true);
rj.error = true;
rj.running = false;
- completeStatus(rj, response, "" + getStage(stg)
- + "failed. Reason below:\n");
+ completeStatus(rj, response,
+ "" + getStage(stg) + "failed. Reason below:\n");
break;
default:
// Some other response. Probably need to pop up the content in a window.
rj.setSubmitted(true);
try
{
- completeStatus(
- rj,
- response,
- ""
- + getStage(stg)
- + " resulted in an unexpected server response.<br/>Url concerned was <a href=\""
- + request.getURI()
- + "\">"
- + request.getURI()
- + "</a><br/>Filtered response content below:<br/>");
+ completeStatus(rj, response, "" + getStage(stg)
+ + " resulted in an unexpected server response.<br/>Url concerned was <a href=\""
+ + request.getURI() + "\">" + request.getURI()
+ + "</a><br/>Filtered response content below:<br/>");
} catch (IOException e)
{
Cache.log.debug("IOException when consuming unhandled response",
} catch (Error ex)
{
- Cache.log.warn("Failed to finish parsing data for job "
- + rj.getJobId());
+ Cache.log.warn(
+ "Failed to finish parsing data for job " + rj.getJobId());
ex.printStackTrace();
} catch (Exception ex)
{
- Cache.log.warn("Failed to finish parsing data for job "
- + rj.getJobId());
+ Cache.log.warn(
+ "Failed to finish parsing data for job " + rj.getJobId());
ex.printStackTrace();
} finally
{
rj.error = true;
rj.statMessage = "Error whilst parsing data for this job.<br>URL for job response is :<a href=\""
- + rj.resSet.getUrl()
- + "\">"
- + rj.resSet.getUrl()
+ + rj.resSet.getUrl() + "\">" + rj.resSet.getUrl()
+ "</a><br>";
}
}
{
destAl = restClient.av.getAlignment();
destHCs = restClient.av.getAlignment().getHiddenColumns();
- resultDest
- .add(restClient.isShowResultsInNewView() ? AddDataTo.newView
- : AddDataTo.currentView);
+ resultDest.add(restClient.isShowResultsInNewView()
+ ? AddDataTo.newView
+ : AddDataTo.currentView);
destPanels.add(restClient.recoverAlignPanelForView());
}
else
{
// TODO: decide if multiple multiple alignments returned by
// non-vseparable services are allowed.
- Cache.log
- .warn("dealing with multiple alignment products returned by non-vertically separable service.");
+ Cache.log.warn(
+ "dealing with multiple alignment products returned by non-vertically separable service.");
}
// recover reference to last alignment created for this rest frame
// ready for extension
destColsel.add(destHCs);
resultDest.add(AddDataTo.newAlignment);
throw new Error(
- MessageManager
- .getString("error.implementation_error")
+ MessageManager.getString("error.implementation_error")
+ "TODO: ");
}
}
}
else
{
- Cache.log
- .warn("Couldn't resolve original sequence for new sequence.");
+ Cache.log.warn(
+ "Couldn't resolve original sequence for new sequence.");
}
}
if (sg.hasSeqrep())
{
// adjust boundaries of recovered group w.r.t. new group being
// merged on to original alignment.
- int start = sg.getStartRes() + contigs[ncnt], end = sg
- .getEndRes() + contigs[ncnt];
+ int start = sg.getStartRes() + contigs[ncnt],
+ end = sg.getEndRes() + contigs[ncnt];
if (start < exsg.getStartRes())
{
exsg.setStartRes(start);
grass = groupNames.get(alan[nrj][an].groupRef.getName());
if (grass == null)
{
- Cache.log
- .error("Couldn't relocate group referemce for group "
+ Cache.log.error(
+ "Couldn't relocate group referemce for group "
+ alan[nrj][an].groupRef.getName());
}
}
visan.sequenceRef = sqass;
visAlAn.add(visan);
}
- if (contigs[ncnt] + alan[nrj][an].annotations.length > visan.annotations.length)
+ if (contigs[ncnt]
+ + alan[nrj][an].annotations.length > visan.annotations.length)
{
// increase width of annotation row
Annotation[] newannv = new Annotation[contigs[ncnt]
{
// TODO: process each newick file, lifting over sequence refs to
// current alignment, if necessary.
- Cache.log
- .error("Tree recovery from restjob not yet implemented.");
+ Cache.log.error(
+ "Tree recovery from restjob not yet implemented.");
}
}
}
{
AlignmentI destal;
HiddenColumns destcs;
- String alTitle = MessageManager.formatMessage(
- "label.webservice_job_title_on", new String[] {
- restClient.service.details.Action,
+ String alTitle = MessageManager
+ .formatMessage("label.webservice_job_title_on", new String[]
+ { restClient.service.details.Action,
restClient.service.details.Name, restClient.viewTitle });
switch (action)
{
destcs = destColsel.get(als);
destaf = new AlignFrame(destal, destcs, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
- PaintRefresher.Refresh(destaf, destaf.getViewport()
- .getSequenceSetId());
+ PaintRefresher.Refresh(destaf,
+ destaf.getViewport().getSequenceSetId());
// todo transfer any feature settings and colouring
/*
* destaf.getFeatureRenderer().transferSettings(this.featureSettings);
{
if (start + width < end)
{
- blocks[c][s] = sequenceIs[s].getSubSequence(start, start
- + width);
+ blocks[c][s] = sequenceIs[s].getSubSequence(start,
+ start + width);
}
else
{
boolean diff = (gapCharacter != other.gapCharacter);
diff |= vseparable != other.vseparable;
diff |= hseparable != other.hseparable;
- diff |= !(urlSuffix == null && other.urlSuffix == null || (urlSuffix != null
- && other.urlSuffix != null && urlSuffix.equals(other.urlSuffix)));
+ diff |= !(urlSuffix == null && other.urlSuffix == null
+ || (urlSuffix != null && other.urlSuffix != null
+ && urlSuffix.equals(other.urlSuffix)));
// TODO - robust diff that includes constants and reordering of URL
// diff |= !(postUrl.equals(other.postUrl));
// diff |= !inputParams.equals(other.inputParams);
resultData.add(JvDataType.valueOf(tok = st.nextToken()));
} catch (NoSuchElementException x)
{
- warnings.append("Invalid result type: '" + tok
- + "' (must be one of: ");
+ warnings.append(
+ "Invalid result type: '" + tok + "' (must be one of: ");
String sep = "";
for (JvDataType vl : JvDataType.values())
{
;
vls.add(new String("gapCharacter='" + gapCharacter + "'"));
vls.add(new String("returns='" + _genOutputFormatString() + "'"));
- return StringUtils
- .arrayToSeparatorList(vls.toArray(new String[0]), ",");
+ return StringUtils.arrayToSeparatorList(vls.toArray(new String[0]),
+ ",");
}
public String toString()
* @param p
* @return
*/
- protected int parseServiceList(String[] list, StringBuffer warnings, int p)
+ protected int parseServiceList(String[] list, StringBuffer warnings,
+ int p)
{
boolean invalid = false;
// look for the first non-empty position - expect it to be service name
&& list[p + 4].trim().length() > 5)
{
urlSuffix = null;
- invalid |= !configureFromInputParamEncodedUrl(list[p + 4], warnings);
+ invalid |= !configureFromInputParamEncodedUrl(list[p + 4],
+ warnings);
p += 5;
}
}
iprmparams = iprm.substring(colon + 1);
iprm = iprm.substring(0, colon);
}
- valid = parseTypeString(prms.group(0), tok, iprm, iprmparams,
- iparams, warnings);
+ valid = parseTypeString(prms.group(0), tok, iprm, iprmparams, iparams,
+ warnings);
}
if (valid)
{
// TODO - find a better way of maintaining this classlist
return new Class[] { jalview.ws.rest.params.Alignment.class,
jalview.ws.rest.params.AnnotationFile.class,
- SeqGroupIndexVector.class,
- jalview.ws.rest.params.SeqIdVector.class,
+ SeqGroupIndexVector.class, jalview.ws.rest.params.SeqIdVector.class,
jalview.ws.rest.params.SeqVector.class,
jalview.ws.rest.params.Tree.class };
}
/**
* search the input types for an instance of the given class
*
- * @param <validInput.inputType> class1
+ * @param <validInput.inputType>
+ * class1
* @return
*/
public boolean inputInvolves(Class<?> class1)
try
{
File fa = File.createTempFile("jvmime", ".fa");
- PrintWriter pw = new PrintWriter(
- new OutputStreamWriter(new BufferedOutputStream(
- new FileOutputStream(fa)), "UTF-8"));
- pw.append(new FormatAdapter().formatSequences(format,
- alignment, jvsuffix));
+ PrintWriter pw = new PrintWriter(new OutputStreamWriter(
+ new BufferedOutputStream(new FileOutputStream(fa)),
+ "UTF-8"));
+ pw.append(new FormatAdapter().formatSequences(format, alignment,
+ jvsuffix));
pw.close();
return new FileBody(fa, "text/plain");
} catch (Exception ex)
return true;
}
}
- warnings.append("Invalid alignment format '" + val
- + "'. Must be one of (");
+ warnings.append(
+ "Invalid alignment format '" + val + "'. Must be one of (");
for (String fmt : FileFormats.getInstance().getWritableFormats(true))
{
warnings.append(" ").append(fmt);
return true;
} catch (Exception x)
{
- warnings.append("Invalid molecule type '" + val
- + "'. Must be one of (");
+ warnings.append(
+ "Invalid molecule type '" + val + "'. Must be one of (");
for (molType v : molType.values())
{
warnings.append(" " + v);
"Append jalview style /start-end suffix to ID", false, false,
writeAsFile, null));
- List<String> writable = FileFormats
- .getInstance().getWritableFormats(true);
+ List<String> writable = FileFormats.getInstance()
+ .getWritableFormats(true);
lst.add(new Option("format", "Alignment upload format", true,
- FileFormat.Fasta.toString(), format.getName(), writable,
+ FileFormat.Fasta.toString(), format.getName(), writable, null));
+ lst.add(createMolTypeOption("type", "Sequence type", false, type,
null));
- lst.add(createMolTypeOption("type", "Sequence type", false, type, null));
return lst;
}
AlignmentI al = rj.getAlignmentForInput(token, molType.MIX);
if (format.equals(JVANNOT))
{
- return new StringBody(
- new jalview.io.AnnotationFile()
- .printAnnotationsForAlignment(al));
+ return new StringBody(new jalview.io.AnnotationFile()
+ .printAnnotationsForAlignment(al));
}
else
{
"Unrecognised format for exporting Annotation (" + format
+ ")");
}
- return new StringBody(
- new jalview.io.AnnotationFile().printCSVAnnotations(al
- .getAlignmentAnnotation()));
+ return new StringBody(new jalview.io.AnnotationFile()
+ .printCSVAnnotations(al.getAlignmentAnnotation()));
}
}
{
// TODO - consider disregarding base options here.
List<OptionI> lst = getBaseOptions();
- lst.add(new Option("format", "Alignment annotation upload format",
- true, JVANNOT, format, Arrays.asList(new String[] { JVANNOT,
- CSVANNOT }), null));
+ lst.add(new Option("format", "Alignment annotation upload format", true,
+ JVANNOT, format, Arrays.asList(new String[]
+ { JVANNOT, CSVANNOT }), null));
return lst;
}
}
prm.add(URLEncoder.encode(value, "UTF-8"));
} catch (UnsupportedEncodingException ex)
{
- throw new Error(MessageManager.formatMessage(
- "error.couldnt_encode_as_utf8", new String[] { value }), ex);
+ throw new Error(MessageManager
+ .formatMessage("error.couldnt_encode_as_utf8", new String[]
+ { value }), ex);
}
}
{
if (tokenstring.size() > 1)
{
- warnings.append("IMPLEMENTATION ERROR: Constant POST parameters cannot have more than one value.");
+ warnings.append(
+ "IMPLEMENTATION ERROR: Constant POST parameters cannot have more than one value.");
return false;
}
if (tokenstring.size() == 1)
public boolean configureProperty(String tok, String val,
StringBuffer warnings)
{
- warnings.append("IMPLEMENTATION ERROR: No Properties to configure for a Constant parameter.");
+ warnings.append(
+ "IMPLEMENTATION ERROR: No Properties to configure for a Constant parameter.");
return false;
}
* @author JimP
*
*/
-public class SeqGroupIndexVector extends InputType implements
- AlignmentProcessor
+public class SeqGroupIndexVector extends InputType
+ implements AlignmentProcessor
{
public SeqGroupIndexVector()
{
{
if (sg.getSize() < minsize)
{
- throw new NoValidInputDataException(
- MessageManager
- .formatMessage(
- "exception.notvaliddata_group_contains_less_than_min_seqs",
- new String[] { Integer.valueOf(minsize)
- .toString() }));
+ throw new NoValidInputDataException(MessageManager.formatMessage(
+ "exception.notvaliddata_group_contains_less_than_min_seqs",
+ new String[]
+ { Integer.valueOf(minsize).toString() }));
}
// TODO: refactor to sequenceGroup for efficiency -
// getAlignmentRowInterval(AlignmentI al)
return true;
} catch (Exception x)
{
- warnings.append("Invalid molecule type '" + val
- + "'. Must be one of (");
+ warnings.append(
+ "Invalid molecule type '" + val + "'. Must be one of (");
for (molType v : molType.values())
{
warnings.append(" " + v);
List<OptionI> lst = getBaseOptions();
lst.add(new Option("sep",
"Separator character between elements of vector", true, ",",
- sep, Arrays.asList(new String[] { " ", ",", ";", "\t", "|" }),
- null));
+ sep, Arrays.asList(new String[]
+ { " ", ",", ";", "\t", "|" }), null));
lst.add(new IntegerParameter("minsize",
"Minimum size of partition allowed by service", true, 1,
minsize, 1, 0));
return true;
} catch (Exception x)
{
- warnings.append("Invalid molecule type '" + val
- + "'. Must be one of (");
+ warnings.append(
+ "Invalid molecule type '" + val + "'. Must be one of (");
for (molType v : molType.values())
{
warnings.append(" " + v);
List<OptionI> lst = getBaseOptions();
lst.add(new Option("sep",
"Separator character between elements of vector", true, ",",
- sep, Arrays.asList(new String[] { " ", ",", ";", "\t", "|" }),
+ sep, Arrays.asList(new String[]
+ { " ", ",", ";", "\t", "|" }), null));
+ lst.add(createMolTypeOption("type", "Sequence type", false, type,
null));
- lst.add(createMolTypeOption("type", "Sequence type", false, type, null));
return lst;
}
}
return true;
} catch (Exception x)
{
- warnings.append("Invalid molecule type '" + val
- + "'. Must be one of (");
+ warnings.append(
+ "Invalid molecule type '" + val + "'. Must be one of (");
for (molType v : molType.values())
{
warnings.append(" " + v);
List<OptionI> lst = getBaseOptions();
lst.add(new Option("sep",
"Separator character between elements of vector", true, ",",
- sep, Arrays.asList(new String[] { " ", ",", ";", "\t", "|" }),
- null));
+ sep, Arrays.asList(new String[]
+ { " ", ",", ";", "\t", "|" }), null));
lst.add(createMolTypeOption("type", "Sequence type", false, type,
molType.MIX));
/*
* rj.getTreeForInput(token); return new StringBody(new )
*/
- throw new Error(
- MessageManager
- .getString("error.tree_inputtype_not_yet_implemented"));
+ throw new Error(MessageManager
+ .getString("error.tree_inputtype_not_yet_implemented"));
// return null;
}
{
return null;
}
- String[] sf = fetchableDbs.keySet().toArray(
- new String[fetchableDbs.size()]);
+ String[] sf = fetchableDbs.keySet()
+ .toArray(new String[fetchableDbs.size()]);
return sf;
}
seqset = fetcher.getSequenceRecords(qsb.toString());
} catch (Exception ex)
{
- System.err.println("Failed to retrieve the following from "
- + db);
+ System.err.println(
+ "Failed to retrieve the following from " + db);
System.err.println(qsb);
ex.printStackTrace(System.err);
}
for (int is = 0; is < seqs.length; is++)
{
rseqs.addElement(seqs[is]);
- List<DBRefEntry> frefs = DBRefUtils.searchRefs(seqs[is]
- .getDBRefs(), new DBRefEntry(db, null, null));
+ List<DBRefEntry> frefs = DBRefUtils.searchRefs(
+ seqs[is].getDBRefs(),
+ new DBRefEntry(db, null, null));
for (DBRefEntry dbr : frefs)
{
queriesFound.add(dbr.getAccessionId());
{
if (fetcher.getRawRecords() != null)
{
- System.out.println("# Retrieved from " + db + ":"
- + qsb.toString());
+ System.out.println(
+ "# Retrieved from " + db + ":" + qsb.toString());
StringBuffer rrb = fetcher.getRawRecords();
/*
* for (int rr = 0; rr<rrb.length; rr++) {
Exception ex)
{
- System.err.println("Failed to retrieve the following references from "
- + db);
+ System.err.println(
+ "Failed to retrieve the following references from " + db);
int n = 0;
for (String qv : queriesMade)
{
} catch (Exception e)
{
// Serious problems if this happens.
- throw new Error(
- MessageManager
- .getString("error.dbrefsource_implementation_exception"),
- e);
+ throw new Error(MessageManager
+ .getString("error.dbrefsource_implementation_exception"), e);
}
addDbRefSourceImpl(proxy);
}
{
fetchableDbs = new Hashtable<String, Map<String, DbSourceProxy>>();
}
- Map<String, DbSourceProxy> slist = fetchableDbs.get(proxy
- .getDbSource());
+ Map<String, DbSourceProxy> slist = fetchableDbs
+ .get(proxy.getDbSource());
if (slist == null)
{
fetchableDbs.put(proxy.getDbSource(),
/**
* select sources which are implemented by instances of the given class
*
- * @param class that implements DbSourceProxy
+ * @param class
+ * that implements DbSourceProxy
* @return null or vector of source names for fetchers
*/
public String[] getDbInstances(Class class1)
{
if (!DbSourceProxy.class.isAssignableFrom(class1))
{
- throw new Error(
- MessageManager
- .formatMessage(
- "error.implementation_error_dbinstance_must_implement_interface",
- new String[] { class1.toString() }));
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_error_dbinstance_must_implement_interface",
+ new String[]
+ { class1.toString() }));
}
if (fetchableDbs == null)
{
if (format != null)
{
sequences = new FormatAdapter().readFile(result.toString(),
- DataSourceType.PASTE,
- format);
+ DataSourceType.PASTE, format);
}
return sequences;
}
public void setSeqName(String seqName)
{
- this.seqName = (seqName.length() > MAX_ID_LENGTH) ? seqName.substring(
- 0, MAX_ID_LENGTH) : seqName;
+ this.seqName = (seqName.length() > MAX_ID_LENGTH)
+ ? seqName.substring(0, MAX_ID_LENGTH)
+ : seqName;
}
public String getSeqResidue()
public void setStrName(String strName)
{
- this.strName = (strName.length() > MAX_ID_LENGTH) ? strName.substring(
- 0, MAX_ID_LENGTH) : strName;
+ this.strName = (strName.length() > MAX_ID_LENGTH)
+ ? strName.substring(0, MAX_ID_LENGTH)
+ : strName;
}
public String getStrResidue()
private enum ResidueDetailType
{
- NAME_SEC_STRUCTURE("nameSecondaryStructure"), CODE_SEC_STRUCTURE(
- "codeSecondaryStructure"), ANNOTATION("Annotation");
+ NAME_SEC_STRUCTURE("nameSecondaryStructure"),
+ CODE_SEC_STRUCTURE("codeSecondaryStructure"), ANNOTATION("Annotation");
private String code;
private ResidueDetailType(String code)
try
{
attr = Files.readAttributes(filePath, BasicFileAttributes.class);
- diffInDays = (int) ((new Date().getTime() - attr.lastModifiedTime()
- .toMillis()) / (1000 * 60 * 60 * 24));
+ diffInDays = (int) ((new Date().getTime()
+ - attr.lastModifiedTime().toMillis())
+ / (1000 * 60 * 60 * 24));
// System.out.println("Diff in days : " + diffInDays);
} catch (IOException e)
{
* @throws SiftsException
* @throws IOException
*/
- public static File downloadSiftsFile(String pdbId) throws SiftsException,
- IOException
+ public static File downloadSiftsFile(String pdbId)
+ throws SiftsException, IOException
{
if (pdbId.contains(".cif"))
{
}
outputStream.close();
inputStream.close();
-// System.out.println(">>> File downloaded : " + downloadedSiftsFile
-// + " took " + (System.currentTimeMillis() - now) + "ms");
+ // System.out.println(">>> File downloaded : " + downloadedSiftsFile
+ // + " took " + (System.currentTimeMillis() - now) + "ms");
return new File(downloadedSiftsFile);
}
{
continue;
}
- String canonicalSource = DBRefUtils.getCanonicalName(dbRef
- .getSource());
+ String canonicalSource = DBRefUtils
+ .getCanonicalName(dbRef.getSource());
if (isValidDBRefEntry(dbRef)
- && (canonicalSource.equalsIgnoreCase(DBRefSource.UNIPROT) || canonicalSource
- .equalsIgnoreCase(DBRefSource.PDB)))
+ && (canonicalSource.equalsIgnoreCase(DBRefSource.UNIPROT)
+ || canonicalSource.equalsIgnoreCase(DBRefSource.PDB)))
{
return dbRef;
}
int orignalSeqStart = seq.getStart();
if (orignalSeqStart >= 1)
{
- int subSeqStart = (seqStart >= orignalSeqStart) ? seqStart
- - orignalSeqStart : 0;
+ int subSeqStart = (seqStart >= orignalSeqStart)
+ ? seqStart - orignalSeqStart
+ : 0;
int subSeqEnd = seqEnd - (orignalSeqStart - 1);
subSeqEnd = originalSeq.length() < subSeqEnd ? originalSeq.length()
: subSeqEnd;
{
pdbRefDb = cRefDb;
}
- if (cRefDb.getDbCoordSys()
- .equalsIgnoreCase(seqCoordSys.getName())
+ if (cRefDb.getDbCoordSys().equalsIgnoreCase(seqCoordSys.getName())
&& isAccessionMatched(cRefDb.getDbAccessionId()))
{
- currSeqIndex = getLeadingIntegerValue(
- cRefDb.getDbResNum(), UNASSIGNED);
+ currSeqIndex = getLeadingIntegerValue(cRefDb.getDbResNum(),
+ UNASSIGNED);
if (pdbRefDb != null)
{
break;// exit loop if pdb and uniprot are already found
if (currSeqIndex >= seq.getStart() && currSeqIndex <= seq.getEnd())
{
- int resNum = (pdbRefDb == null) ? getLeadingIntegerValue(
- residue.getDbResNum(), UNASSIGNED)
+ int resNum = (pdbRefDb == null)
+ ? getLeadingIntegerValue(residue.getDbResNum(),
+ UNASSIGNED)
: getLeadingIntegerValue(pdbRefDb.getDbResNum(),
UNASSIGNED);
omitNonObserved.add(currSeqIndex);
++nonObservedShiftIndex;
}
- mapping.put(currSeqIndex - nonObservedShiftIndex, new int[] {
- Integer.valueOf(resNum), UNASSIGNED });
+ mapping.put(currSeqIndex - nonObservedShiftIndex,
+ new int[]
+ { Integer.valueOf(resNum), UNASSIGNED });
}
}
}
return failValue;
}
-
/**
*
* @param chainId
*/
public Entity getEntityByMostOptimalMatchedId(String chainId)
{
- // System.out.println("---> advanced greedy entityId matching block entered..");
+ // System.out.println("---> advanced greedy entityId matching block
+ // entered..");
List<Entity> entities = siftsEntry.getEntity();
SiftsEntitySortPojo[] sPojo = new SiftsEntitySortPojo[entities.size()];
int count = 0;
return null;
}
- private class SiftsEntitySortPojo implements
- Comparable<SiftsEntitySortPojo>
+ private class SiftsEntitySortPojo
+ implements Comparable<SiftsEntitySortPojo>
{
public String entityId;
private int nonObservedShiftIndex;
- public SegmentHelperPojo(SequenceI seq,
- HashMap<Integer, int[]> mapping,
+ public SegmentHelperPojo(SequenceI seq, HashMap<Integer, int[]> mapping,
TreeMap<Integer, String> resNumMap,
List<Integer> omitNonObserved, int nonObservedShiftIndex)
{
// output mappings
StringBuilder output = new StringBuilder(512);
output.append(NEWLINE);
- output.append("Sequence \u27f7 Structure mapping details").append(
- NEWLINE);
+ output.append("Sequence \u27f7 Structure mapping details")
+ .append(NEWLINE);
output.append("Method: SIFTS");
output.append(NEWLINE).append(NEWLINE);
for (int j = 0; j < nochunks; j++)
{
// Print the first aligned sequence
- output.append(new Format("%" + (maxid) + "s").form(seqName)).append(
- " ");
+ output.append(new Format("%" + (maxid) + "s").form(seqName))
+ .append(" ");
for (int i = 0; i < len; i++)
{
{
throw new SiftsException(">>> Low PID detected for SIFTs mapping...");
}
- output.append("Length of alignment = " + seqRes.length()).append(
- NEWLINE);
+ output.append("Length of alignment = " + seqRes.length())
+ .append(NEWLINE);
output.append(new Format("Percentage ID = %2.2f").form(pid));
return output;
}
}
} catch (IOException e)
{
- System.out
- .println("Exception while closing download file output stream: "
+ System.out.println(
+ "Exception while closing download file output stream: "
+ e.getMessage());
}
try
} catch (IOException e)
{
System.out.println("Exception while closing download channel: "
- + e.getMessage());
+ + e.getMessage());
}
try
{
} catch (IOException e)
{
System.out.println("Exception while deleting download temp file: "
- + e.getMessage());
+ + e.getMessage());
}
}
}
git://source.jalview.org / jalview.git / commitdiff