* JarOutputStream
*
* @param ap
- * panel to create jalview model for
+ * panel to create jalview model for
* @param fileName
- * name of alignment panel written to output stream
+ * name of alignment panel written to output stream
* @param jout
- * jar output stream
+ * jar output stream
* @param out
- * jar entry name
+ * jar entry name
*/
public JalviewModel SaveState(AlignmentPanel ap, String fileName,
JarOutputStream jout)
AppJmol jmol;
// This must have been loaded, is it still visible?
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
- String matchedFile=null;
+ String matchedFile = null;
for (int f = frames.length - 1; f > -1; f--)
{
if (frames[f] instanceof AppJmol)
{
jmol = (AppJmol) frames[f];
- if (!jmol.pdbentry.getId().equals(entry.getId())
- && !(entry.getId().length()>4
- && entry.getId().toLowerCase().startsWith(jmol.pdbentry.getId().toLowerCase())))
+ if (!jmol.pdbentry.getId().equals(entry.getId())
+ && !(entry.getId().length() > 4 && entry.getId()
+ .toLowerCase().startsWith(
+ jmol.pdbentry.getId().toLowerCase())))
continue;
- matchedFile = jmol.pdbentry.getFile(); // record the file so we can get at it if the ID match is ambiguous (e.g. 1QIP==1qipA)
+ matchedFile = jmol.pdbentry.getFile(); // record the file so we
+ // can get at it if the ID
+ // match is ambiguous (e.g.
+ // 1QIP==1qipA)
StructureState state = new StructureState();
state.setVisible(true);
state.setXpos(jmol.getX());
}
}
- if (matchedFile!=null || entry.getFile() != null )
+ if (matchedFile != null || entry.getFile() != null)
{
- if (entry.getFile()!=null)
+ if (entry.getFile() != null)
{
// use entry's file
matchedFile = entry.getFile();
- }
+ }
pdb.setFile(matchedFile); // entry.getFile());
if (pdbfiles == null)
{
for (int p = 0; p < jac[i].aaWidth; p++)
{
Alcodon cmap = new Alcodon();
- if (jac[i].codons[p]!=null)
+ if (jac[i].codons[p] != null)
{
- // Null codons indicate a gapped column in the translated peptide alignment.
+ // Null codons indicate a gapped column in the translated peptide
+ // alignment.
cmap.setPos1(jac[i].codons[p][0]);
cmap.setPos2(jac[i].codons[p][1]);
cmap.setPos3(jac[i].codons[p][2]);
for (int m = 0; m < pmaps.length; m++)
{
AlcodMap alcmap = new AlcodMap();
- alcmap.setDnasq(seqHash(dnas[m]));
+ alcmap.setDnasq(seqHash(dnas[m]));
alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
false));
alc.addAlcodMap(alcmap);
if (av.hasHiddenColumns)
{
- for (int c = 0; c < av.getColumnSelection().getHiddenColumns().size(); c++)
+ if (av.getColumnSelection() == null
+ || av.getColumnSelection().getHiddenColumns() == null)
{
- int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
- .elementAt(c);
- HiddenColumns hc = new HiddenColumns();
- hc.setStart(region[0]);
- hc.setEnd(region[1]);
- view.addHiddenColumns(hc);
+ warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
+ }
+ else
+ {
+ for (int c = 0; c < av.getColumnSelection().getHiddenColumns()
+ .size(); c++)
+ {
+ int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
+ .elementAt(c);
+ HiddenColumns hc = new HiddenColumns();
+ hc.setStart(region[0]);
+ hc.setEnd(region[1]);
+ view.addHiddenColumns(hc);
+ }
}
}
* exist, the result of the hashcode call for the object.
*
* @param jvobj
- * jalview data object
+ * jalview data object
* @return unique ID for referring to jvobj
*/
private String makeHashCode(Object jvobj, String altCode)
* return local jalview object mapped to ID, if it exists
*
* @param idcode
- * (may be null)
+ * (may be null)
* @return null or object bound to idcode
*/
private Object retrieveExistingObj(String idcode)
/**
* Load a jalview project archive from a jar file
*
- * @param file -
- * HTTP URL or filename
+ * @param file
+ * - HTTP URL or filename
*/
public AlignFrame LoadJalviewAlign(final String file)
{
* Load alignment frame from jalview XML DOM object
*
* @param object
- * DOM
+ * DOM
* @param file
- * filename source string
+ * filename source string
* @param loadTreesAndStructures
- * when false only create Viewport
+ * when false only create Viewport
* @param jprovider
- * data source provider
+ * data source provider
* @return alignment frame created from view stored in DOM
*/
AlignFrame LoadFromObject(JalviewModel object, String file,
Alcodon[] alcods = alc[i].getAlcodon();
for (int p = 0; p < cf.codons.length; p++)
{
- if (alcods[p].hasPos1() && alcods[p].hasPos2() && alcods[p].hasPos3())
+ if (alcods[p].hasPos1() && alcods[p].hasPos2()
+ && alcods[p].hasPos3())
{
// translated codons require three valid positions
cf.codons[p] = new int[3];
cf.codons[p][0] = (int) alcods[p].getPos1();
cf.codons[p][1] = (int) alcods[p].getPos2();
cf.codons[p][2] = (int) alcods[p].getPos3();
- } else {
+ }
+ else
+ {
cf.codons[p] = null;
}
}
sg.textColour = new java.awt.Color(groups[i].getTextCol1());
sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
- sg.setShowunconserved(groups[i].hasShowUnconserved() ? groups[i].isShowUnconserved() : false);
+ sg.setShowunconserved(groups[i].hasShowUnconserved() ? groups[i]
+ .isShowUnconserved() : false);
sg.thresholdTextColour = groups[i].getTextColThreshold();
if (groups[i].getConsThreshold() != 0)
else
{
// update local tree attributes ?
- // TODO: should check if tp has been manipulated by user - if so its settings shouldn't be modified
+ // 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.treeCanvas.ap = ap; // af.alignPanel;
}
- if (tp==null)
+ if (tp == null)
{
- warn("There was a problem recovering stored Newick tree: \n"+tree.getNewick());
+ warn("There was a problem recovering stored Newick tree: \n"
+ + tree.getNewick());
continue;
}
{
// create a new Jmol window
String state = ids[p].getStructureState(s).getContent();
- StringBuffer newFileLoc=null;
- if (state.indexOf("load")>-1) {
- newFileLoc = new StringBuffer(state.substring(
- 0, state.indexOf("\"", state.indexOf("load")) + 1));
-
- newFileLoc.append(jpdb.getFile());
- newFileLoc.append(state.substring(state.indexOf("\"", state
- .indexOf("load \"") + 6)));
- } else {
- System.err.println("Ignoring incomplete Jmol state for PDB "+ids[p].getId());
-
+ StringBuffer newFileLoc = null;
+ if (state.indexOf("load") > -1)
+ {
+ newFileLoc = new StringBuffer(state.substring(0, state
+ .indexOf("\"", state.indexOf("load")) + 1));
+
+ newFileLoc.append(jpdb.getFile());
+ newFileLoc.append(state.substring(state.indexOf("\"",
+ state.indexOf("load \"") + 6)));
+ }
+ else
+ {
+ System.err
+ .println("Ignoring incomplete Jmol state for PDB "
+ + ids[p].getId());
+
newFileLoc = new StringBuffer(state);
newFileLoc.append("; load \"");
newFileLoc.append(jpdb.getFile());
newFileLoc.append("\";");
}
-
- if (newFileLoc!=null) {
+
+ if (newFileLoc != null)
+ {
new AppJmol(pdbFile, ids[p].getId(), seq, af.alignPanel,
- newFileLoc.toString(), new java.awt.Rectangle(x, y,
- width, height), sviewid);
+ newFileLoc.toString(), new java.awt.Rectangle(x,
+ y, width, height), sviewid);
}
}
af.viewport.textColour = new java.awt.Color(view.getTextCol1());
af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
af.viewport.thresholdTextColour = view.getTextColThreshold();
- af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view.isShowUnconserved() : false);
+ af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view
+ .isShowUnconserved() : false);
af.viewport.setStartRes(view.getStartRes());
af.viewport.setStartSeq(view.getStartSeq());
/*
* if
- * (view.getAnnotationColours().getColourScheme().equals("None")) {
- * sg.cs = new AnnotationColourGradient(
+ * (view.getAnnotationColours().getColourScheme().equals("None"
+ * )) { sg.cs = new AnnotationColourGradient(
* af.viewport.alignment.getAlignmentAnnotation()[i], new
* java.awt.Color(view.getAnnotationColours(). getMinColour()),
* new java.awt.Color(view.getAnnotationColours().
Setting setting = jms.getFeatureSettings().getSetting(fs);
if (setting.hasMincolour())
{
- // TODO: determine how to set data independent bounds for a graduated colour scheme's range.
- GraduatedColor gc = new GraduatedColor(new java.awt.Color(setting.getMincolour()), new java.awt.Color(setting.getColour()),
- 0,1);
- if (setting.hasThreshold()) {
+ // TODO: determine how to set data independent bounds for a graduated
+ // colour scheme's range.
+ GraduatedColor gc = new GraduatedColor(new java.awt.Color(setting
+ .getMincolour()),
+ new java.awt.Color(setting.getColour()), 0, 1);
+ if (setting.hasThreshold())
+ {
gc.setThresh(setting.getThreshold());
gc.setThreshType(setting.getThreshstate());
}
- } else {
+ }
+ else
+ {
af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
- setting.getType(), new java.awt.Color(setting.getColour()));
+ setting.getType(),
+ new java.awt.Color(setting.getColour()));
}
renderOrder[fs] = setting.getType();
if (setting.hasOrder())
SequenceI[] dsseqs = new SequenceI[dseqs.size()];
dseqs.copyInto(dsseqs);
ds = new jalview.datamodel.Alignment(dsseqs);
- debug("Created new dataset "+vamsasSet.getDatasetId()+" for alignment "+System.identityHashCode(al));
+ debug("Created new dataset " + vamsasSet.getDatasetId()
+ + " for alignment " + System.identityHashCode(al));
addDatasetRef(vamsasSet.getDatasetId(), ds);
}
// set the dataset for the newly imported alignment.
/**
*
* @param vamsasSeq
- * sequence definition to create/merge dataset sequence for
+ * sequence definition to create/merge dataset sequence for
* @param ds
- * dataset alignment
+ * dataset alignment
* @param dseqs
- * vector to add new dataset sequence to
+ * vector to add new dataset sequence to
*/
private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
AlignmentI ds, Vector dseqs)
}
java.util.Hashtable datasetIds = null;
+
java.util.IdentityHashMap dataset2Ids = null;
+
private Alignment getDatasetFor(String datasetId)
{
if (datasetIds == null)
}
datasetIds.put(datasetId, dataset);
}
+
/**
* make a new dataset ID for this jalview dataset alignment
+ *
* @param dataset
* @return
*/
private String getDatasetIdRef(jalview.datamodel.Alignment dataset)
{
- if (dataset.getDataset()!=null)
+ if (dataset.getDataset() != null)
{
warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
}
- String datasetId=makeHashCode(dataset, null);
- if (datasetId==null)
+ String datasetId = makeHashCode(dataset, null);
+ if (datasetId == null)
{
// make a new datasetId and record it
if (dataset2Ids == null)
{
dataset2Ids = new IdentityHashMap();
- } else {
+ }
+ else
+ {
datasetId = (String) dataset2Ids.get(dataset);
}
- if (datasetId==null)
+ if (datasetId == null)
{
- datasetId = "ds"+dataset2Ids.size()+1;
- dataset2Ids.put(dataset,datasetId);
+ datasetId = "ds" + dataset2Ids.size() + 1;
+ dataset2Ids.put(dataset, datasetId);
}
}
return datasetId;
}
+
private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
{
for (int d = 0; d < sequence.getDBRefCount(); d++)
MappingChoice mc = m.getMappingChoice();
if (mc.getDseqFor() != null)
{
- String dsfor = ""+mc.getDseqFor();
+ String dsfor = "" + mc.getDseqFor();
if (seqRefIds.containsKey(dsfor))
{
/**
else
{
uniqueSetSuffix = "";
- jm.getJalviewModelSequence().getViewport(0).setId(null); // we don't overwrite the view we just copied
+ jm.getJalviewModelSequence().getViewport(0).setId(null); // we don't
+ // overwrite the
+ // view we just
+ // copied
}
- if (this.frefedSequence==null)
+ if (this.frefedSequence == null)
{
frefedSequence = new Vector();
}
af.closeMenuItem_actionPerformed(true);
/*
- * if(ap.av.alignment.getAlignmentAnnotation()!=null) { for(int i=0; i<ap.av.alignment.getAlignmentAnnotation().length;
- * i++) { if(!ap.av.alignment.getAlignmentAnnotation()[i].autoCalculated) {
+ * if(ap.av.alignment.getAlignmentAnnotation()!=null) { for(int i=0;
+ * i<ap.av.alignment.getAlignmentAnnotation().length; i++) {
+ * if(!ap.av.alignment.getAlignmentAnnotation()[i].autoCalculated) {
* af.alignPanel.av.alignment.getAlignmentAnnotation()[i] =
* ap.av.alignment.getAlignmentAnnotation()[i]; } } }
*/
private void debug(String string)
{
- debug(string,null);
+ debug(string, null);
}
+
private void debug(String msg, Exception e)
{
if (Cache.log != null)
* alignment objects containing dataset sequences
*
* @param vobj2jv
- * Map from ID strings to jalview datamodel
+ * Map from ID strings to jalview datamodel
* @param jv2vobj
- * Map from jalview datamodel to ID strings
+ * Map from jalview datamodel to ID strings
*
*
*/
git://source.jalview.org / jalview.git / commitdiff