an.setCentreColLabels(aa[i].centreColLabels);
an.setScaleColLabels(aa[i].scaleColLabel);
an.setShowAllColLabels(aa[i].showAllColLabels);
-
+
if (aa[i].graph > 0)
{
an.setGraph(true);
an.addAnnotationElement(ae);
if (aa[i].autoCalculated)
{
- // only write one non-null entry into the annotation row - sufficient to get the visualization attributes necessary to display data
+ // only write one non-null entry into the annotation row -
+ // sufficient to get the visualization attributes necessary to
+ // display data
continue;
}
}
Vector settingsAdded = new Vector();
Object gstyle = null;
GraduatedColor gcol = null;
- for (int ro = 0; ro < renderOrder.length; ro++)
+ if (renderOrder != null)
{
- gstyle = ap.seqPanel.seqCanvas.getFeatureRenderer()
- .getFeatureStyle(renderOrder[ro]);
- Setting setting = new Setting();
- setting.setType(renderOrder[ro]);
- if (gstyle instanceof GraduatedColor)
- {
- gcol = (GraduatedColor) gstyle;
- setting.setColour(gcol.getMaxColor().getRGB());
- setting.setMincolour(gcol.getMinColor().getRGB());
- setting.setMin(gcol.getMin());
- setting.setMax(gcol.getMax());
- setting.setColourByLabel(gcol.isColourByLabel());
- setting.setAutoScale(gcol.isAutoScale());
- setting.setThreshold(gcol.getThresh());
- setting.setThreshstate(gcol.getThreshType());
- }
- else
+ for (int ro = 0; ro < renderOrder.length; ro++)
{
- setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
- .getColour(renderOrder[ro]).getRGB());
- }
+ gstyle = ap.seqPanel.seqCanvas.getFeatureRenderer()
+ .getFeatureStyle(renderOrder[ro]);
+ Setting setting = new Setting();
+ setting.setType(renderOrder[ro]);
+ if (gstyle instanceof GraduatedColor)
+ {
+ gcol = (GraduatedColor) gstyle;
+ setting.setColour(gcol.getMaxColor().getRGB());
+ setting.setMincolour(gcol.getMinColor().getRGB());
+ setting.setMin(gcol.getMin());
+ setting.setMax(gcol.getMax());
+ setting.setColourByLabel(gcol.isColourByLabel());
+ setting.setAutoScale(gcol.isAutoScale());
+ setting.setThreshold(gcol.getThresh());
+ setting.setThreshstate(gcol.getThreshType());
+ }
+ else
+ {
+ setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
+ .getColour(renderOrder[ro]).getRGB());
+ }
- setting.setDisplay(av.featuresDisplayed
- .containsKey(renderOrder[ro]));
- float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
- renderOrder[ro]);
- if (rorder > -1)
- {
- setting.setOrder(rorder);
+ setting.setDisplay(av.featuresDisplayed
+ .containsKey(renderOrder[ro]));
+ float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer()
+ .getOrder(renderOrder[ro]);
+ if (rorder > -1)
+ {
+ setting.setOrder(rorder);
+ }
+ fs.addSetting(setting);
+ settingsAdded.addElement(renderOrder[ro]);
}
- fs.addSetting(setting);
- settingsAdded.addElement(renderOrder[ro]);
}
// Make sure we save none displayed feature settings
/**
* store any annotations which forward reference a group's ID
*/
- Hashtable<String,ArrayList<jalview.datamodel.AlignmentAnnotation>> groupAnnotRefs = new Hashtable<String,ArrayList<jalview.datamodel.AlignmentAnnotation>>();
+ Hashtable<String, ArrayList<jalview.datamodel.AlignmentAnnotation>> groupAnnotRefs = new Hashtable<String, ArrayList<jalview.datamodel.AlignmentAnnotation>>();
if (vamsasSet.getAnnotationCount() > 0)
{
an[i].setAutoCalculated(true);
}
}
- if (autoForView || (an[i].hasAutoCalculated() && an[i].isAutoCalculated())) {
+ if (autoForView
+ || (an[i].hasAutoCalculated() && an[i].isAutoCalculated()))
+ {
// remove ID - we don't recover annotation from other views for
// view-specific annotation
an[i].setId(null);
if (an[i].getGraph())
{
- float llim=0,hlim=0;
- // if (autoForView || an[i].isAutoCalculated()) {
- // hlim=11f;
- // }
+ float llim = 0, hlim = 0;
+ // if (autoForView || an[i].isAutoCalculated()) {
+ // hlim=11f;
+ // }
jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
- an[i].getDescription(), anot, llim, hlim, an[i].getGraphType());
+ an[i].getDescription(), anot, llim, hlim,
+ an[i].getGraphType());
jaa.graphGroup = an[i].getGraphGroup();
an[i].getThresholdLine().getColour())));
}
- if (autoForView || an[i].isAutoCalculated()) {
- // Hardwire the symbol display line to ensure that labels for histograms are displayed
- jaa.hasText=true;
+ if (autoForView || an[i].isAutoCalculated())
+ {
+ // Hardwire the symbol display line to ensure that labels for
+ // histograms are displayed
+ jaa.hasText = true;
}
}
else
// and make a note of any group association
if (an[i].getGroupRef() != null && an[i].getGroupRef().length() > 0)
{
- ArrayList<jalview.datamodel.AlignmentAnnotation> aal=groupAnnotRefs.get(an[i].getGroupRef());
- if (aal==null) {
+ ArrayList<jalview.datamodel.AlignmentAnnotation> aal = groupAnnotRefs
+ .get(an[i].getGroupRef());
+ if (aal == null)
+ {
aal = new ArrayList<jalview.datamodel.AlignmentAnnotation>();
- groupAnnotRefs.put(an[i].getGroupRef(),aal);
+ groupAnnotRefs.put(an[i].getGroupRef(), aal);
}
aal.add(jaa);
}
if (jaa.autoCalculated)
{
autoAlan.add(new JvAnnotRow(i, jaa));
- } else
+ }
+ else
// if (!autoForView)
{
- // add autocalculated group annotation and any user created annotation for the view
+ // add autocalculated group annotation and any user created annotation
+ // for the view
al.addAnnotation(jaa);
}
}
.get(groups[i].getId());
if (jaal != null)
{
- for (jalview.datamodel.AlignmentAnnotation jaa:jaal) {
+ for (jalview.datamodel.AlignmentAnnotation jaa : jaal)
+ {
jaa.groupRef = sg;
if (jaa.autoCalculated)
{
- // match up and try to set group autocalc alignment row for this annotation
- if (jaa.label.startsWith("Consensus for ")) {
+ // match up and try to set group autocalc alignment row for this
+ // annotation
+ if (jaa.label.startsWith("Consensus for "))
+ {
sg.setConsensus(jaa);
}
- // match up and try to set group autocalc alignment row for this annotation
- if (jaa.label.startsWith("Conservation for ")) {
+ // match up and try to set group autocalc alignment row for this
+ // annotation
+ if (jaa.label.startsWith("Conservation for "))
+ {
sg.setConservationRow(jaa);
- }
}
+ }
}
}
}
{ x, y, width, height }, "",
new Hashtable<String, Object[]>(), new boolean[]
{ false, false, true } });
- // Legacy pre-2.7 conversion JAL-823 :
- // do not assume any view has to be linked for colour by sequence
+ // Legacy pre-2.7 conversion JAL-823 :
+ // do not assume any view has to be linked for colour by
+ // sequence
}
-
+
// assemble String[] { pdb files }, String[] { id for each
// file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
// seqs_file 2}, boolean[] {
.getStructureState(s).getColourwithAlignPanel()
: false;
// default for pre-2.7 projects is that Jmol colouring is enabled
- ((boolean[])jmoldat[3])[2] &=ids[p].getStructureState(s).hasColourByJmol() ? ids[p].getStructureState(s).getColourByJmol() : true;
+ ((boolean[]) jmoldat[3])[2] &= ids[p].getStructureState(s)
+ .hasColourByJmol() ? ids[p].getStructureState(s)
+ .getColourByJmol() : true;
if (((String) jmoldat[1]).length() < ids[p]
.getStructureState(s).getContent().length())
}
else
{
- errorMessage=("The Jmol views in the Jalview 2 project may\nnot be correctly bound to sequences in the alignment.\nIn the case of problems, see note at\nhttp://issues.jalview.org/browse/JAL-747");
+ errorMessage = ("The Jmol views in the Jalview 2 project may\nnot be correctly bound to sequences in the alignment.\nIn the case of problems, see note at\nhttp://issues.jalview.org/browse/JAL-747");
warn(errorMessage);
}
}
int[] geom = (int[]) svattrib[0];
String state = (String) svattrib[1];
Hashtable<String, Object[]> oldFiles = (Hashtable<String, Object[]>) svattrib[2];
- final boolean useinJmolsuperpos = ((boolean[]) svattrib[3])[0], usetoColourbyseq = ((boolean[]) svattrib[3])[1], jmolColouring=((boolean[])svattrib[3])[2];
+ final boolean useinJmolsuperpos = ((boolean[]) svattrib[3])[0], usetoColourbyseq = ((boolean[]) svattrib[3])[1], jmolColouring = ((boolean[]) svattrib[3])[2];
int x = geom[0], y = geom[1], width = geom[2], height = geom[3];
// collate the pdbfile -> sequence mappings from this view
Vector<String> pdbfilenames = new Vector<String>();
try
{
sview = new AppJmol(pdbf, id, sq, alf.alignPanel,
- useinJmolsuperpos, usetoColourbyseq, jmolColouring, fileloc,
- rect, vid);
+ useinJmolsuperpos, usetoColourbyseq,
+ jmolColouring, fileloc, rect, vid);
} catch (OutOfMemoryError ex)
{
new OOMWarning("restoring structure view for PDB id "
SequenceI[] seq = (SequenceI[]) ((Vector<SequenceI>) filedat[2])
.toArray(new SequenceI[0]);
((AppJmol) comp).jmb.ssm.setMapping(seq, null, pdbFile,
- jalview.io.AppletFormatAdapter.FILE);
+ jalview.io.AppletFormatAdapter.FILE);
((AppJmol) comp).jmb.addSequenceForStructFile(pdbFile, seq);
}
// and add the AlignmentPanel's reference to the Jmol view
}
if (usetoColourbyseq)
{
- ((AppJmol) comp).useAlignmentPanelForColourbyseq(ap, !jmolColouring);
+ ((AppJmol) comp).useAlignmentPanelForColourbyseq(ap,
+ !jmolColouring);
}
else
{
Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
view.getHeight());
af.alignPanel.updateAnnotation(false); // recompute any autoannotation
- reorderAutoannotation(af,al,autoAlan);
+ reorderAutoannotation(af, al, autoAlan);
return af;
}
private void reorderAutoannotation(AlignFrame af, Alignment al,
ArrayList<JvAnnotRow> autoAlan)
{
- // copy over visualization settings for autocalculated annotation in the
+ // copy over visualization settings for autocalculated annotation in the
// view
if (al.getAlignmentAnnotation() != null)
{
if (valan != null)
{
// delete the auto calculated row from the alignment
- al.deleteAnnotation(al.getAlignmentAnnotation()[h],false);
+ al.deleteAnnotation(al.getAlignmentAnnotation()[h], false);
hSize--;
h--;
if (valan != nullAnnot)
{
- if (jalan!=valan.template) {
+ if (jalan != valan.template)
+ {
// newly created autoannotation row instance
// so keep a reference to the visible annotation row
// and copy over all relevant attributes
- if (valan.template.graphHeight >= 0)
-
- {
- jalan.graphHeight = valan.template.graphHeight;
- }
- jalan.visible = valan.template.visible;
+ if (valan.template.graphHeight >= 0)
+
+ {
+ jalan.graphHeight = valan.template.graphHeight;
+ }
+ jalan.visible = valan.template.visible;
}
reorder.add(new JvAnnotRow(valan.order, jalan));
}
}
}
}
- int s=0,srt[] = new int[reorder.size()];
+ int s = 0, srt[] = new int[reorder.size()];
JvAnnotRow[] rws = new JvAnnotRow[reorder.size()];
- for (JvAnnotRow jvar:reorder) {
+ for (JvAnnotRow jvar : reorder)
+ {
rws[s] = jvar;
- srt[s++]=jvar.order;
+ srt[s++] = jvar.order;
}
reorder.clear();
jalview.util.QuickSort.sort(srt, rws);
git://source.jalview.org / jalview.git / commitdiff