/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
import java.awt.Rectangle;
import java.io.*;
+import java.lang.reflect.InvocationTargetException;
import java.net.*;
import java.util.*;
+import java.util.Map.Entry;
import java.util.jar.*;
import javax.swing.*;
import uk.ac.vamsas.objects.utils.MapList;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.schemabinding.version2.*;
* will be :)
*
* @author $author$
- * @version $Revision$
+ * @version $Revision: 1.134 $
*/
public class Jalview2XML
{
JarOutputStream jout)
{
initSeqRefs();
-
+ Vector jmolViewIds = new Vector(); //
Vector userColours = new Vector();
AlignViewport av = ap.av;
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())))
- continue;
- 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());
- state.setYpos(jmol.getY());
- state.setWidth(jmol.getWidth());
- state.setHeight(jmol.getHeight());
- state.setViewId(jmol.getViewId());
- String statestring = jmol.viewer.getStateInfo();
- if (state != null)
- {
- state.setContent(statestring.replaceAll("\n", ""));
- }
- for (int s = 0; s < jmol.sequence.length; s++)
+ for (int peid = 0; peid < jmol.jmb.pdbentry.length; peid++)
{
- if (jal.findIndex(jmol.sequence[s]) > -1)
+ if (!jmol.jmb.pdbentry[peid].getId().equals(entry.getId())
+ && !(entry.getId().length() > 4 && entry
+ .getId()
+ .toLowerCase()
+ .startsWith(
+ jmol.jmb.pdbentry[peid].getId()
+ .toLowerCase())))
+ continue;
+ if (matchedFile == null)
+ {
+ matchedFile = jmol.jmb.pdbentry[peid].getFile();
+ }
+ else if (!matchedFile.equals(jmol.jmb.pdbentry[peid]
+ .getFile()))
{
- pdb.addStructureState(state);
+ Cache.log
+ .warn("Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
+ + jmol.jmb.pdbentry[peid].getFile());
+ ; // record the
+ }
+ // file so we
+ // can get at it if the ID
+ // match is ambiguous (e.g.
+ // 1QIP==1qipA)
+ String statestring = jmol.jmb.viewer.getStateInfo();
+
+ for (int smap = 0; smap < jmol.jmb.sequence[peid].length; smap++)
+ {
+ if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
+ {
+ StructureState state = new StructureState();
+ state.setVisible(true);
+ state.setXpos(jmol.getX());
+ state.setYpos(jmol.getY());
+ state.setWidth(jmol.getWidth());
+ state.setHeight(jmol.getHeight());
+ state.setViewId(jmol.getViewId());
+ state.setAlignwithAlignPanel(jmol.isUsedforaligment(ap));
+ state.setColourwithAlignPanel(jmol
+ .isUsedforcolourby(ap));
+ state.setColourByJmol(jmol.isColouredByJmol());
+ if (!jmolViewIds.contains(state.getViewId()))
+ {
+ // Make sure we only store a Jmol state once in each XML
+ // document.
+ jmolViewIds.addElement(state.getViewId());
+ state.setContent(statestring.replaceAll("\n", ""));
+ }
+ else
+ {
+ state.setContent("# duplicate state");
+ }
+ pdb.addStructureState(state);
+ }
}
}
}
}
an.setGroupRef(groupIdr.toString());
}
- if (aa[i] == av.quality || aa[i] == av.conservation
- || aa[i] == av.consensus || aa[i].autoCalculated)
- {
- // new way of indicating autocalculated annotation -
- an.setAutoCalculated(aa[i].autoCalculated);
- // write a stub for this annotation - indicate presence of autocalc
- // rows
- an.setLabel(aa[i].label);
- an.setGraph(true);
- vamsasSet.addAnnotation(an);
- continue;
- }
+
+ // store all visualization attributes for annotation
+ an.setGraphHeight(aa[i].graphHeight);
+ an.setCentreColLabels(aa[i].centreColLabels);
+ an.setScaleColLabels(aa[i].scaleColLabel);
+ an.setShowAllColLabels(aa[i].showAllColLabels);
if (aa[i].graph > 0)
{
}
an.setLabel(aa[i].label);
+
+ if (aa[i] == av.quality || aa[i] == av.conservation
+ || aa[i] == av.consensus || aa[i].autoCalculated)
+ {
+ // new way of indicating autocalculated annotation -
+ an.setAutoCalculated(aa[i].autoCalculated);
+ }
if (aa[i].hasScore())
{
an.setScore(aa[i].getScore());
ae.setPosition(a);
if (aa[i].annotations[a].secondaryStructure != ' '
&& aa[i].annotations[a].secondaryStructure != '\0')
- ae
- .setSecondaryStructure(aa[i].annotations[a].secondaryStructure
- + "");
+ ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure
+ + "");
if (aa[i].annotations[a].colour != null
&& aa[i].annotations[a].colour != java.awt.Color.black)
}
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
+ continue;
+ }
}
}
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());
view.setViewName(av.viewName);
view.setGatheredViews(av.gatherViewsHere);
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
}
Group g = new Group();
g.setName(grp);
- g
- .setDisplay(((Boolean) ap.seqPanel.seqCanvas
- .getFeatureRenderer().featureGroups.get(grp))
- .booleanValue());
+ g.setDisplay(((Boolean) ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups
+ .get(grp)).booleanValue());
fs.addGroup(g);
groupsAdded.addElement(grp);
}
return null;
}
+ private class JvAnnotRow
+ {
+ public JvAnnotRow(int i, AlignmentAnnotation jaa)
+ {
+ order = i;
+ template = jaa;
+ }
+
+ /**
+ * persisted version of annotation row from which to take vis properties
+ */
+ public jalview.datamodel.AlignmentAnnotation template;
+
+ /**
+ * original position of the annotation row in the alignment
+ */
+ public int order;
+ }
+
/**
* Load alignment frame from jalview XML DOM object
*
// ////////////////////////////////
// LOAD ANNOTATIONS
- boolean hideQuality = true, hideConservation = true, hideConsensus = true;
+ ArrayList<JvAnnotRow> autoAlan = new ArrayList<JvAnnotRow>();
/**
* store any annotations which forward reference a group's ID
*/
- Hashtable groupAnnotRefs = new Hashtable();
+ Hashtable<String, ArrayList<jalview.datamodel.AlignmentAnnotation>> groupAnnotRefs = new Hashtable<String, ArrayList<jalview.datamodel.AlignmentAnnotation>>();
if (vamsasSet.getAnnotationCount() > 0)
{
for (int i = 0; i < an.length; i++)
{
- // set visibility for automatic annotation for this view
- if (an[i].getLabel().equals("Quality"))
- {
- hideQuality = false;
- continue;
- }
- else if (an[i].getLabel().equals("Conservation"))
- {
- hideConservation = false;
- continue;
+ /**
+ * test if annotation is automatically calculated for this view only
+ */
+ boolean autoForView = false;
+ if (an[i].getLabel().equals("Quality")
+ || an[i].getLabel().equals("Conservation")
+ || an[i].getLabel().equals("Consensus"))
+ {
+ // Kludge for pre 2.5 projects which lacked the autocalculated flag
+ autoForView = true;
+ if (!an[i].hasAutoCalculated())
+ {
+ an[i].setAutoCalculated(true);
+ }
}
- else if (an[i].getLabel().equals("Consensus"))
+ if (autoForView
+ || (an[i].hasAutoCalculated() && an[i].isAutoCalculated()))
{
- hideConsensus = false;
- continue;
+ // remove ID - we don't recover annotation from other views for
+ // view-specific annotation
+ an[i].setId(null);
}
+
// set visiblity for other annotation in this view
if (an[i].getId() != null
&& annotationIds.containsKey(an[i].getId()))
if (!an[i].getScoreOnly())
{
anot = new jalview.datamodel.Annotation[al.getWidth()];
-
for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
{
if (ae[aa].getPosition() >= anot.length)
anot[ae[aa].getPosition()] = 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].getValue()
+ ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
+ (ae[aa].getSecondaryStructure() == null || ae[aa]
+ .getSecondaryStructure().length() == 0) ? ' '
+ : ae[aa].getSecondaryStructure().charAt(0),
+ ae[aa].getValue()
);
// JBPNote: Consider verifying dataflow for IO of secondary
// {
// anot[ae[aa].getPosition()].displayCharacter = "";
// }
- anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa]
- .getColour());
+ anot[ae[aa].getPosition()].colour = new java.awt.Color(
+ ae[aa].getColour());
}
}
jalview.datamodel.AlignmentAnnotation jaa = null;
if (an[i].getGraph())
{
+ float llim = 0, hlim = 0;
+ // if (autoForView || an[i].isAutoCalculated()) {
+ // hlim=11f;
+ // }
jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
- an[i].getDescription(), anot, 0, 0, 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;
+ }
}
else
{
jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
an[i].getDescription(), anot);
}
- // register new annotation
- if (an[i].getId() != null)
+ if (autoForView)
{
- annotationIds.put(an[i].getId(), jaa);
- jaa.annotationId = an[i].getId();
- }
- // recover sequence association
- if (an[i].getSequenceRef() != null)
- {
- if (al.findName(an[i].getSequenceRef()) != null)
+ // register new annotation
+ if (an[i].getId() != null)
+ {
+ annotationIds.put(an[i].getId(), jaa);
+ jaa.annotationId = an[i].getId();
+ }
+ // recover sequence association
+ if (an[i].getSequenceRef() != null)
{
- jaa.createSequenceMapping(al.findName(an[i].getSequenceRef()),
- 1, true);
- al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
+ if (al.findName(an[i].getSequenceRef()) != null)
+ {
+ jaa.createSequenceMapping(
+ al.findName(an[i].getSequenceRef()), 1, true);
+ al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(
+ jaa);
+ }
}
}
// and make a note of any group association
if (an[i].getGroupRef() != null && an[i].getGroupRef().length() > 0)
{
- groupAnnotRefs.put(an[i].getGroupRef(), jaa);
+ 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);
+ }
+ aal.add(jaa);
}
if (an[i].hasScore())
jaa.autoCalculated = true; // means annotation will be marked for
// update at end of load.
}
- al.addAnnotation(jaa);
+ if (an[i].hasGraphHeight())
+ {
+ jaa.graphHeight = an[i].getGraphHeight();
+ }
+ if (jaa.autoCalculated)
+ {
+ autoAlan.add(new JvAnnotRow(i, jaa));
+ }
+ else
+ // if (!autoForView)
+ {
+ // add autocalculated group annotation and any user created annotation
+ // for the view
+ al.addAnnotation(jaa);
+ }
}
}
groups[i].getDisplayText(), groups[i].getColourText(),
groups[i].getStart(), groups[i].getEnd());
- sg
- .setOutlineColour(new java.awt.Color(groups[i]
- .getOutlineColour()));
+ sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));
sg.textColour = new java.awt.Color(groups[i].getTextCol1());
sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
sg.thresholdTextColour = groups[i].getTextColThreshold();
if (groups[i].hasShowConsensusHistogram())
{
- sg
- .setShowConsensusHistogram(groups[i]
- .isShowConsensusHistogram());
+ sg.setShowConsensusHistogram(groups[i].isShowConsensusHistogram());
}
;
if (groups[i].hasShowSequenceLogo())
{
- sg.setIncludeAllConsSymbols(groups[i].isShowSequenceLogo());
+ sg.setshowSequenceLogo(groups[i].isShowSequenceLogo());
}
if (groups[i].hasIgnoreGapsinConsensus())
{
if (groups[i].getConsThreshold() != 0)
{
jalview.analysis.Conservation c = new jalview.analysis.Conservation(
- "All", ResidueProperties.propHash, 3, sg
- .getSequences(null), 0, sg.getWidth() - 1);
+ "All", ResidueProperties.propHash, 3,
+ sg.getSequences(null), 0, sg.getWidth() - 1);
c.calculate();
c.verdict(false, 25);
sg.cs.setConservation(c);
if (groups[i].getId() != null && groupAnnotRefs.size() > 0)
{
// re-instate unique group/annotation row reference
- jalview.datamodel.AlignmentAnnotation jaa = (jalview.datamodel.AlignmentAnnotation) groupAnnotRefs
+ ArrayList<jalview.datamodel.AlignmentAnnotation> jaal = groupAnnotRefs
.get(groups[i].getId());
- if (jaa != null)
+ if (jaal != null)
{
- jaa.groupRef = sg;
+ 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 "))
+ {
+ sg.setConsensus(jaa);
+ }
+ // match up and try to set group autocalc alignment row for this
+ // annotation
+ if (jaa.label.startsWith("Conservation for "))
+ {
+ sg.setConservationRow(jaa);
+ }
+ }
+ }
}
}
al.addGroup(sg);
if (isnewview)
{
- af = loadViewport(file, JSEQ, hiddenSeqs, al, hideConsensus,
- hideQuality, hideConservation, jms, view, uniqueSeqSetId,
- viewId);
+ af = loadViewport(file, JSEQ, hiddenSeqs, al, jms, view,
+ uniqueSeqSetId, viewId, autoAlan);
av = af.viewport;
ap = af.alignPanel;
}
TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
if (tp == null)
{
- tp = af.ShowNewickTree(new jalview.io.NewickFile(tree
- .getNewick()), tree.getTitle(), tree.getWidth(), tree
- .getHeight(), tree.getXpos(), tree.getYpos());
+ tp = af.ShowNewickTree(
+ new jalview.io.NewickFile(tree.getNewick()),
+ tree.getTitle(), tree.getWidth(), tree.getHeight(),
+ tree.getXpos(), tree.getYpos());
if (tree.getId() != null)
{
// perhaps bind the tree id to something ?
// //LOAD STRUCTURES
if (loadTreesAndStructures)
{
+ // run through all PDB ids on the alignment, and collect mappings between
+ // jmol view ids and all sequences referring to it
+ Hashtable<String, Object[]> jmolViewIds = new Hashtable();
+
for (int i = 0; i < JSEQ.length; i++)
{
if (JSEQ[i].getPdbidsCount() > 0)
int y = ids[p].getStructureState(s).getYpos();
int width = ids[p].getStructureState(s).getWidth();
int height = ids[p].getStructureState(s).getHeight();
- AppJmol comp = null;
- JInternalFrame[] frames = null;
- do
+
+ // Probably don't need to do this anymore...
+ // Desktop.desktop.getComponentAt(x, y);
+ // TODO: NOW: check that this recovers the PDB file correctly.
+ String pdbFile = loadPDBFile(jprovider, ids[p].getId());
+ jalview.datamodel.SequenceI seq = (jalview.datamodel.SequenceI) seqRefIds
+ .get(JSEQ[i].getId() + "");
+ if (sviewid == null)
+ {
+ sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width
+ + "," + height;
+ }
+ if (!jmolViewIds.containsKey(sviewid))
+ {
+ jmolViewIds.put(sviewid, new Object[]
+ { new int[]
+ { 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
+ }
+
+ // assemble String[] { pdb files }, String[] { id for each
+ // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
+ // seqs_file 2}, boolean[] {
+ // linkAlignPanel,superposeWithAlignpanel}} from hash
+ Object[] jmoldat = (Object[]) jmolViewIds.get(sviewid);
+ ((boolean[]) jmoldat[3])[0] |= ids[p].getStructureState(s)
+ .hasAlignwithAlignPanel() ? ids[p].getStructureState(
+ s).getAlignwithAlignPanel() : false;
+ // never colour by linked panel if not specified
+ ((boolean[]) jmoldat[3])[1] |= ids[p].getStructureState(s)
+ .hasColourwithAlignPanel() ? ids[p]
+ .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;
+
+ if (((String) jmoldat[1]).length() < ids[p]
+ .getStructureState(s).getContent().length())
{
- try
- {
- frames = Desktop.desktop.getAllFrames();
- } catch (ArrayIndexOutOfBoundsException e)
{
- // occasional No such child exceptions are thrown here...
- frames = null;
- try
- {
- Thread.sleep(10);
- } catch (Exception f)
- {
- }
- ;
+ jmoldat[1] = ids[p].getStructureState(s).getContent();
}
- } while (frames == null);
- // search for any Jmol windows already open from other
- // alignment views that exactly match the stored structure state
- for (int f = 0; comp == null && f < frames.length; f++)
+ }
+ if (ids[p].getFile() != null)
{
- if (frames[f] instanceof AppJmol)
+ Object[] seqstrmaps = (Object[]) ((Hashtable) jmoldat[2])
+ .get(ids[p].getFile());
+ if (seqstrmaps == null)
{
- if (sviewid != null
- && ((AppJmol) frames[f]).getViewId().equals(
- sviewid))
- {
- // post jalview 2.4 schema includes structure view id
- comp = (AppJmol) frames[f];
- }
- else if (frames[f].getX() == x && frames[f].getY() == y
- && frames[f].getHeight() == height
- && frames[f].getWidth() == width)
- {
- comp = (AppJmol) frames[f];
- }
+ ((Hashtable) jmoldat[2]).put(
+ new File(ids[p].getFile()).toString(),
+ seqstrmaps = new Object[]
+ { pdbFile, ids[p].getId(), new Vector(),
+ new Vector() });
+ }
+ if (!((Vector) seqstrmaps[2]).contains(seq))
+ {
+ ((Vector) seqstrmaps[2]).addElement(seq);
+ // ((Vector)seqstrmaps[3]).addElement(n) :
+ // in principle, chains
+ // should be stored here : do we need to
+ // TODO: store and recover seq/pdb_id :
+ // chain mappings
}
}
- // Probably don't need to do this anymore...
- // Desktop.desktop.getComponentAt(x, y);
- // TODO: NOW: check that this recovers the PDB file correctly.
- String pdbFile = loadPDBFile(jprovider, ids[p].getId());
+ else
+ {
+ errorMessage = ("The Jmol views in this project were imported\nfrom an older version of Jalview.\nPlease review the sequence colour associations\nin the Colour by section of the Jmol View menu.\n\nIn the case of problems, see note at\nhttp://issues.jalview.org/browse/JAL-747");
+ warn(errorMessage);
+ }
+ }
+ }
+ }
+ }
+ {
- jalview.datamodel.SequenceI[] seq = new jalview.datamodel.SequenceI[]
- { (jalview.datamodel.SequenceI) seqRefIds.get(JSEQ[i].getId()
- + "") };
+ // Instantiate the associated Jmol views
+ for (Entry<String, Object[]> entry : jmolViewIds.entrySet())
+ {
+ String sviewid = entry.getKey();
+ Object[] svattrib = entry.getValue();
+ 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];
+ 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>();
+ Vector<SequenceI[]> seqmaps = new Vector<SequenceI[]>();
+ Vector<String> pdbids = new Vector<String>();
- if (comp == null)
+ // Search to see if we've already created this Jmol view
+ AppJmol comp = null;
+ JInternalFrame[] frames = null;
+ do
+ {
+ try
+ {
+ frames = Desktop.desktop.getAllFrames();
+ } catch (ArrayIndexOutOfBoundsException e)
+ {
+ // occasional No such child exceptions are thrown here...
+ frames = null;
+ try
{
- // 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));
+ Thread.sleep(10);
+ } catch (Exception f)
+ {
+ }
+ ;
+ }
+ } while (frames == null);
+ // search for any Jmol windows already open from other
+ // alignment views that exactly match the stored structure state
+ for (int f = 0; comp == null && f < frames.length; f++)
+ {
+ if (frames[f] instanceof AppJmol)
+ {
+ if (sviewid != null
+ && ((AppJmol) frames[f]).getViewId().equals(sviewid))
+ {
+ // post jalview 2.4 schema includes structure view id
+ comp = (AppJmol) frames[f];
+ }
+ else if (frames[f].getX() == x && frames[f].getY() == y
+ && frames[f].getHeight() == height
+ && frames[f].getWidth() == width)
+ {
+ comp = (AppJmol) frames[f];
+ }
+ }
+ }
- 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());
+ if (comp == null)
+ {
+ // create a new Jmol window.
+ // First parse the Jmol state to translate filenames loaded into the
+ // view, and record the order in which files are shown in the Jmol
+ // view, so we can add the sequence mappings in same order.
+ StringBuffer newFileLoc = null;
+ int cp = 0, ncp, ecp;
+ while ((ncp = state.indexOf("load ", cp)) > -1)
+ {
+ if (newFileLoc == null)
+ {
+ newFileLoc = new StringBuffer();
+ }
+ newFileLoc.append(state.substring(cp,
+ ncp = (state.indexOf("\"", ncp + 1) + 1)));
+ String oldfilenam = state.substring(ncp,
+ ecp = state.indexOf("\"", ncp));
+ // recover the new mapping data for this old filename
+ // have to normalize filename - since Jmol and jalview do filename
+ // translation differently.
+ Object[] filedat = oldFiles.get(new File(oldfilenam)
+ .toString());
+ newFileLoc.append(((String) filedat[0]));
+ pdbfilenames.addElement((String) filedat[0]);
+ pdbids.addElement((String) filedat[1]);
+ seqmaps.addElement((SequenceI[]) ((Vector<SequenceI>) filedat[2])
+ .toArray(new SequenceI[0]));
+ newFileLoc.append("\"");
+ cp = ecp + 1; // advance beyond last \" and set cursor so we can
+ // look for next file statement.
+ }
+ if (cp > 0)
+ {
+ // just append rest of state
+ newFileLoc.append(state.substring(cp));
+ }
+ else
+ {
+ System.err
+ .print("Ignoring incomplete Jmol state for PDB ids: ");
+ newFileLoc = new StringBuffer(state);
+ newFileLoc.append("; load append ");
+ for (String id : oldFiles.keySet())
+ {
+ // add this and any other pdb files that should be present in
+ // the viewer
+ Object[] filedat = oldFiles.get(id);
+ String nfilename;
+ newFileLoc.append(((String) filedat[0]));
+ pdbfilenames.addElement((String) filedat[0]);
+ pdbids.addElement((String) filedat[1]);
+ seqmaps.addElement((SequenceI[]) ((Vector<SequenceI>) filedat[2])
+ .toArray(new SequenceI[0]));
+ newFileLoc.append(" \"");
+ newFileLoc.append((String) filedat[0]);
+ newFileLoc.append("\"");
- newFileLoc = new StringBuffer(state);
- newFileLoc.append("; load \"");
- newFileLoc.append(jpdb.getFile());
- newFileLoc.append("\";");
- }
+ }
+ newFileLoc.append(";");
+ }
- if (newFileLoc != null)
+ if (newFileLoc != null)
+ {
+ int histbug = newFileLoc.indexOf("history = ");
+ histbug += 10;
+ int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";",
+ histbug);
+ String val = (diff == -1) ? null : newFileLoc.substring(
+ histbug, diff);
+ if (val != null && val.length() >= 4)
+ {
+ if (val.contains("e"))
{
- new AppJmol(pdbFile, ids[p].getId(), seq, af.alignPanel,
- newFileLoc.toString(), new java.awt.Rectangle(x,
- y, width, height), sviewid);
+ if (val.trim().equals("true"))
+ {
+ val = "1";
+ }
+ else
+ {
+ val = "0";
+ }
+ newFileLoc.replace(histbug, diff, val);
}
-
}
- else
- // if (comp != null)
+ // TODO: assemble String[] { pdb files }, String[] { id for each
+ // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
+ // seqs_file 2}} from hash
+ final String[] pdbf = (String[]) pdbfilenames
+ .toArray(new String[pdbfilenames.size()]), id = (String[]) pdbids
+ .toArray(new String[pdbids.size()]);
+ final SequenceI[][] sq = (SequenceI[][]) seqmaps
+ .toArray(new SequenceI[seqmaps.size()][]);
+ final String fileloc = newFileLoc.toString(), vid = sviewid;
+ final AlignFrame alf = af;
+ final java.awt.Rectangle rect = new java.awt.Rectangle(x, y,
+ width, height);
+ try
{
- // NOTE: if the jalview project is part of a shared session then
- // view synchronization should/could be done here.
-
- // add mapping for this sequence to the already open Jmol
- // instance (if it doesn't already exist)
- // These
- StructureSelectionManager.getStructureSelectionManager()
- .setMapping(seq, null, pdbFile,
- jalview.io.AppletFormatAdapter.FILE);
+ javax.swing.SwingUtilities.invokeAndWait(new Runnable()
+ {
+ public void run()
+ {
+ AppJmol sview = null;
+ try
+ {
+ sview = new AppJmol(pdbf, id, sq, alf.alignPanel,
+ useinJmolsuperpos, usetoColourbyseq,
+ jmolColouring, fileloc, rect, vid);
+ } catch (OutOfMemoryError ex)
+ {
+ new OOMWarning("restoring structure view for PDB id "
+ + id, (OutOfMemoryError) ex.getCause());
+ if (sview != null && sview.isVisible())
+ {
+ sview.closeViewer();
+ sview.setVisible(false);
+ sview.dispose();
+ }
+ }
+ }
+ });
+ } catch (InvocationTargetException ex)
+ {
+ warn("Unexpected error when opening Jmol view.", ex);
- ((AppJmol) comp).addSequence(seq);
+ } catch (InterruptedException e)
+ {
+ // e.printStackTrace();
}
}
+
+ }
+ else
+ // if (comp != null)
+ {
+ // NOTE: if the jalview project is part of a shared session then
+ // view synchronization should/could be done here.
+
+ // add mapping for sequences in this view to an already open Jmol
+ // instance
+ for (String id : oldFiles.keySet())
+ {
+ // add this and any other pdb files that should be present in the
+ // viewer
+ Object[] filedat = oldFiles.get(id);
+ String pdbFile = (String) filedat[0];
+ SequenceI[] seq = (SequenceI[]) ((Vector<SequenceI>) filedat[2])
+ .toArray(new SequenceI[0]);
+ ((AppJmol) comp).jmb.ssm.setMapping(seq, null, pdbFile,
+ jalview.io.AppletFormatAdapter.FILE);
+ ((AppJmol) comp).jmb.addSequenceForStructFile(pdbFile, seq);
+ }
+ // and add the AlignmentPanel's reference to the Jmol view
+ ((AppJmol) comp).addAlignmentPanel(ap);
+ if (useinJmolsuperpos)
+ {
+ ((AppJmol) comp).useAlignmentPanelForSuperposition(ap);
+ }
+ else
+ {
+ ((AppJmol) comp).excludeAlignmentPanelForSuperposition(ap);
+ }
+ if (usetoColourbyseq)
+ {
+ ((AppJmol) comp).useAlignmentPanelForColourbyseq(ap,
+ !jmolColouring);
+ }
+ else
+ {
+ ((AppJmol) comp).excludeAlignmentPanelForColourbyseq(ap);
+ }
}
}
}
}
-
+ // and finally return.
return af;
}
AlignFrame loadViewport(String file, JSeq[] JSEQ, Vector hiddenSeqs,
- Alignment al, boolean hideConsensus, boolean hideQuality,
- boolean hideConservation, JalviewModelSequence jms,
- Viewport view, String uniqueSeqSetId, String viewId)
+ Alignment al, JalviewModelSequence jms, Viewport view,
+ String uniqueSeqSetId, String viewId,
+ ArrayList<JvAnnotRow> autoAlan)
{
AlignFrame af = null;
af = new AlignFrame(al, view.getWidth(), view.getHeight(),
for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
{
- hidden.addSequence(al
- .getSequenceAt(JSEQ[s].getHiddenSequences(r)), false);
+ hidden.addSequence(
+ al.getSequenceAt(JSEQ[s].getHiddenSequences(r)), false);
}
af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
}
af.viewport.hideSequence(hseqs);
}
- // set visibility of annotation in view
- if ((hideConsensus || hideQuality || hideConservation)
- && al.getAlignmentAnnotation() != null)
- {
- int hSize = al.getAlignmentAnnotation().length;
- for (int h = 0; h < hSize; h++)
- {
- if ((hideConsensus && al.getAlignmentAnnotation()[h].label
- .equals("Consensus"))
- || (hideQuality && al.getAlignmentAnnotation()[h].label
- .equals("Quality"))
- || (hideConservation && al.getAlignmentAnnotation()[h].label
- .equals("Conservation")))
- {
- al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
- hSize--;
- h--;
- }
- }
- af.alignPanel.adjustAnnotationHeight();
- }
// recover view properties and display parameters
if (view.getViewName() != null)
{
af.viewport.viewName = view.getViewName();
af.setInitialTabVisible();
}
- af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view
- .getHeight());
+ af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
+ view.getHeight());
af.viewport.setShowAnnotation(view.getShowAnnotation());
af.viewport.setAbovePIDThreshold(view.getPidSelected());
);
}
- if (view.getAnnotationColours().getColourScheme().equals(
- "None"))
+ if (view.getAnnotationColours().getColourScheme()
+ .equals("None"))
{
- cs = new AnnotationColourGradient(af.viewport.alignment
- .getAlignmentAnnotation()[i], new java.awt.Color(
- view.getAnnotationColours().getMinColour()),
+ cs = new AnnotationColourGradient(
+ af.viewport.alignment.getAlignmentAnnotation()[i],
new java.awt.Color(view.getAnnotationColours()
- .getMaxColour()), view
- .getAnnotationColours().getAboveThreshold());
+ .getMinColour()), new java.awt.Color(view
+ .getAnnotationColours().getMaxColour()),
+ view.getAnnotationColours().getAboveThreshold());
}
else if (view.getAnnotationColours().getColourScheme()
.startsWith("ucs"))
{
- cs = new AnnotationColourGradient(af.viewport.alignment
- .getAlignmentAnnotation()[i],
+ cs = new AnnotationColourGradient(
+ af.viewport.alignment.getAlignmentAnnotation()[i],
GetUserColourScheme(jms, view
.getAnnotationColours().getColourScheme()),
view.getAnnotationColours().getAboveThreshold());
}
else
{
- cs = new AnnotationColourGradient(af.viewport.alignment
- .getAlignmentAnnotation()[i], ColourSchemeProperty
- .getColour(al, view.getAnnotationColours()
- .getColourScheme()), view
- .getAnnotationColours().getAboveThreshold());
+ cs = new AnnotationColourGradient(
+ af.viewport.alignment.getAlignmentAnnotation()[i],
+ ColourSchemeProperty.getColour(al, view
+ .getAnnotationColours().getColourScheme()),
+ view.getAnnotationColours().getAboveThreshold());
}
// Also use these settings for all the groups
}
if (view.hasShowSequenceLogo())
{
- af.viewport.setShowSequenceLogo(view.getShowSequenceLogo());
+ af.viewport.showSequenceLogo = view.getShowSequenceLogo();
}
else
{
- af.viewport.setShowSequenceLogo(false);
+ af.viewport.showSequenceLogo = false;
}
if (view.hasShowDbRefTooltip())
{
}
af.setMenusFromViewport(af.viewport);
- // This is done twice - why ?
- af.alignPanel.updateAnnotation(false); // recompute any autoannotation
// TODO: we don't need to do this if the viewport is aready visible.
- Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view
- .getHeight());
+ Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
+ view.getHeight());
af.alignPanel.updateAnnotation(false); // recompute any autoannotation
+ 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
+ // view
+ if (al.getAlignmentAnnotation() != null)
+ {
+ /**
+ * Kludge for magic autoannotation names (see JAL-811)
+ */
+ String[] magicNames = new String[]
+ { "Consensus", "Quality", "Conservation" };
+ JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
+ Hashtable<String, JvAnnotRow> visan = new Hashtable<String, JvAnnotRow>();
+ for (String nm : magicNames)
+ {
+ visan.put(nm, nullAnnot);
+ }
+ for (JvAnnotRow auan : autoAlan)
+ {
+ visan.put(auan.template.label, auan);
+ }
+ int hSize = al.getAlignmentAnnotation().length;
+ ArrayList<JvAnnotRow> reorder = new ArrayList<JvAnnotRow>();
+ for (int h = 0; h < hSize; h++)
+ {
+ jalview.datamodel.AlignmentAnnotation jalan = al
+ .getAlignmentAnnotation()[h];
+ if (jalan.autoCalculated)
+ {
+ JvAnnotRow valan = visan.get(jalan.label);
+ if (valan != null)
+ {
+ // delete the auto calculated row from the alignment
+ al.deleteAnnotation(al.getAlignmentAnnotation()[h], false);
+ hSize--;
+ h--;
+ if (valan != nullAnnot)
+ {
+ 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;
+ }
+ reorder.add(new JvAnnotRow(valan.order, jalan));
+ }
+ }
+ }
+ }
+ int s = 0, srt[] = new int[reorder.size()];
+ JvAnnotRow[] rws = new JvAnnotRow[reorder.size()];
+ for (JvAnnotRow jvar : reorder)
+ {
+ rws[s] = jvar;
+ srt[s++] = jvar.order;
+ }
+ reorder.clear();
+ jalview.util.QuickSort.sort(srt, rws);
+ // and re-insert the annotation at its correct position
+ for (JvAnnotRow jvar : rws)
+ {
+ al.addAnnotation(jvar.template, jvar.order);
+ }
+ af.alignPanel.adjustAnnotationHeight();
+ }
+ }
+
Hashtable skipList = null;
/**
/**
* make a new dataset sequence and add it to refIds hash
*/
- djs = new jalview.datamodel.Sequence(ms.getName(), ms
- .getSequence());
+ djs = new jalview.datamodel.Sequence(ms.getName(),
+ ms.getSequence());
djs.setStart(jmap.getMap().getToLowest());
djs.setEnd(jmap.getMap().getToHighest());
djs.setVamsasId(uniqueSetSuffix + sqid);
git://source.jalview.org / jalview.git / blobdiff