/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*/
package jalview.appletgui;
-import java.io.*;
import java.net.*;
import java.util.*;
import java.awt.event.*;
import jalview.analysis.*;
+import jalview.api.SequenceStructureBinding;
import jalview.bin.JalviewLite;
import jalview.commands.*;
import jalview.datamodel.*;
annotationPanelMenuItem.setState(viewport.showAnnotation);
displayNonconservedMenuItem.setState(viewport.getShowunconserved());
+ followMouseOverFlag.setState(viewport.getFollowHighlight());
+ showGroupConsensus.setState(viewport.showGroupConsensus);
+ showGroupConservation.setState(viewport.showGroupConservation);
+ showConsensusHistogram.setState(viewport.showConsensusHistogram);
+ showSequenceLogo.setState(viewport.showSequenceLogo);
seqLimits.setState(viewport.showJVSuffix);
boolean featuresFile = false;
try
{
- featuresFile = new jalview.io.FeaturesFile(file, type).parse(
- viewport.alignment, alignPanel.seqPanel.seqCanvas
- .getFeatureRenderer().featureColours, featureLinks,
- true);
+ featuresFile = new jalview.io.FeaturesFile(file, type)
+ .parse(viewport.alignment,
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
+ featureLinks, true, viewport.applet.getDefaultParameter("relaxedidmatch", false));
} catch (Exception ex)
{
ex.printStackTrace();
{
mouseOverFlag_stateChanged();
}
-
+ else if (evt.getSource() == showGroupConsensus)
+ {
+ showGroupConsensus_actionPerformed();
+ }
+ else if (evt.getSource() == showGroupConservation)
+ {
+ showGroupConservation_actionPerformed();
+ }
+ else if (evt.getSource() == showSequenceLogo)
+ {
+ showSequenceLogo_actionPerformed();
+ }
+ else if (evt.getSource() == showConsensusHistogram)
+ {
+ showConsensusHistogram_actionPerformed();
+ }
+ else if (evt.getSource() == applyAutoAnnotationSettings)
+ {
+ applyAutoAnnotationSettings_actionPerformed();
+ }
alignPanel.paintAlignment(true);
}
viewport.showAllHiddenSeqs();
alignPanel.paintAlignment(true);
}
+ else if (source == showGroupConsensus)
+ {
+ showGroupConsensus_actionPerformed();
+ }
+ else if (source == showGroupConservation)
+ {
+ showGroupConservation_actionPerformed();
+ }
+ else if (source == showSequenceLogo)
+ {
+ showSequenceLogo_actionPerformed();
+ }
+ else if (source == showConsensusHistogram)
+ {
+ showConsensusHistogram_actionPerformed();
+ }
+ else if (source == applyAutoAnnotationSettings)
+ {
+ applyAutoAnnotationSettings_actionPerformed();
+ }
else if (source == featureSettings)
{
new FeatureSettings(alignPanel);
}
else if (source == alProperties)
{
- StringBuffer contents = new StringBuffer();
-
- float avg = 0;
- int min = Integer.MAX_VALUE, max = 0;
- for (int i = 0; i < viewport.alignment.getHeight(); i++)
- {
- int size = viewport.alignment.getSequenceAt(i).getEnd()
- - viewport.alignment.getSequenceAt(i).getStart();
- avg += size;
- if (size > max)
- max = size;
- if (size < min)
- min = size;
- }
- avg = avg / (float) viewport.alignment.getHeight();
-
- contents.append("\nSequences: " + viewport.alignment.getHeight());
- contents.append("\nMinimum Sequence Length: " + min);
- contents.append("\nMaximum Sequence Length: " + max);
- contents.append("\nAverage Length: " + (int) avg);
-
- if (((Alignment) viewport.alignment).alignmentProperties != null)
- {
- Hashtable props = ((Alignment) viewport.alignment).alignmentProperties;
- Enumeration en = props.keys();
- while (en.hasMoreElements())
- {
- String key = en.nextElement().toString();
- contents.append("\n" + key + "\t" + props.get(key));
- }
- }
-
+ StringBuffer contents = new jalview.io.AlignmentProperties(
+ viewport.alignment).formatAsString();
CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
cap.setText(contents.toString());
Frame frame = new Frame();
else if (source == clustalColour)
{
abovePIDThreshold.setState(false);
- changeColour(new ClustalxColourScheme(viewport.alignment
- .getSequences(), viewport.alignment.getWidth()));
+ changeColour(new ClustalxColourScheme(
+ viewport.alignment.getSequences(),
+ viewport.alignment.getWidth()));
}
else if (source == zappoColour)
{
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Alignment output - "
- + e.getActionCommand(), 600, 500);
- cap.setText(new AppletFormatAdapter().formatSequences(e
- .getActionCommand(), viewport.getAlignment(),
+ jalview.bin.JalviewLite.addFrame(frame,
+ "Alignment output - " + e.getActionCommand(), 600, 500);
+ cap.setText(new AppletFormatAdapter().formatSequences(
+ e.getActionCommand(), viewport.getAlignment(),
viewport.showJVSuffix));
}
String features;
if (format.equalsIgnoreCase("Jalview"))
{
- features = new FeaturesFile().printJalviewFormat(viewport.alignment
- .getSequencesArray(), getDisplayedFeatureCols());
+ features = new FeaturesFile().printJalviewFormat(
+ viewport.alignment.getSequencesArray(),
+ getDisplayedFeatureCols());
}
else
{
- features = new FeaturesFile().printGFFFormat(viewport.alignment
- .getSequencesArray(), getDisplayedFeatureCols());
+ features = new FeaturesFile().printGFFFormat(
+ viewport.alignment.getSequencesArray(),
+ getDisplayedFeatureCols());
}
if (displayTextbox)
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.setEndSeq(viewport.alignment.getHeight());
viewport.alignment.getWidth();
- viewport.firePropertyChange("alignment", null, viewport.alignment
- .getSequences());
+ viewport.firePropertyChange("alignment", null,
+ viewport.alignment.getSequences());
}
{
this.setVisible(false);
}
+ viewport.sendSelection();
+ }
+
+ /**
+ * group consensus toggled
+ *
+ */
+ protected void showGroupConsensus_actionPerformed()
+ {
+ viewport.setShowGroupConsensus(showGroupConsensus.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+
+ }
+
+ /**
+ * group conservation toggled.
+ */
+ protected void showGroupConservation_actionPerformed()
+ {
+ viewport.setShowGroupConservation(showGroupConservation.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
+ * .event.ActionEvent)
+ */
+ protected void showConsensusHistogram_actionPerformed()
+ {
+ viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
+ * .event.ActionEvent)
+ */
+ protected void showSequenceLogo_actionPerformed()
+ {
+ viewport.setShowSequenceLogo(showSequenceLogo.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ protected void applyAutoAnnotationSettings_actionPerformed()
+ {
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
}
protected void makeGrpsFromSelection_actionPerformed()
if (viewport.getSelectionGroup() != null)
{
SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
- viewport.getSequenceSelection(), viewport.getAlignmentView(
- true).getSequenceStrings(viewport.getGapCharacter()),
+ viewport.getSequenceSelection(),
+ viewport.getAlignmentView(true).getSequenceStrings(
+ viewport.getGapCharacter()),
viewport.alignment.getGroups());
viewport.alignment.deleteAllGroups();
viewport.sequenceColours = null;
for (int g = 0; g < gps.length; g++)
{
// gps[g].setShowunconserved(viewport.getShowUnconserved());
- gps[g].setIncludeAllConsSymbols(viewport
- .isIncludeAllConsensusSymbols());
+ gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
viewport.alignment.addGroup(gps[g]);
- Color col = new Color((int) (Math.random() * 255), (int) (Math
- .random() * 255), (int) (Math.random() * 255));
+ Color col = new Color((int) (Math.random() * 255),
+ (int) (Math.random() * 255), (int) (Math.random() * 255));
col = col.brighter();
for (Enumeration sq = gps[g].getSequences(null).elements(); sq
.hasMoreElements(); viewport.setSequenceColour(
;
}
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
- // alignPanel.updateAnnotation();
+ alignPanel.updateAnnotation();
alignPanel.paintAlignment(true);
}
}
viewport.setSelectionGroup(sg);
alignPanel.paintAlignment(true);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ viewport.sendSelection();
}
public void deselectAllSequenceMenuItem_actionPerformed()
alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
alignPanel.paintAlignment(true);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ viewport.sendSelection();
}
public void invertSequenceMenuItem_actionPerformed()
}
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ viewport.sendSelection();
}
public void invertColSel_actionPerformed()
viewport.invertColumnSelection();
alignPanel.paintAlignment(true);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ viewport.sendSelection();
}
void trimAlignment(boolean trimLeft)
{
if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)
{
- newal
- .addAnnotation(viewport.alignment
- .getAlignmentAnnotation()[i]);
+ newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);
}
}
}
newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();
PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
- PaintRefresher.Register(newaf.alignPanel, newaf.alignPanel.av
- .getSequenceSetId());
+ PaintRefresher.Register(newaf.alignPanel,
+ newaf.alignPanel.av.getSequenceSetId());
PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
newaf.alignPanel.av.getSequenceSetId());
Alignment al = (Alignment) viewport.alignment;
Conservation c = new Conservation("All",
- ResidueProperties.propHash, 3, al.getSequences(), 0, al
- .getWidth() - 1);
+ ResidueProperties.propHash, 3, al.getSequences(), 0,
+ al.getWidth() - 1);
c.calculate();
c.verdict(false, viewport.ConsPercGaps);
}
if (cs instanceof ClustalxColourScheme)
{
- sg.cs = new ClustalxColourScheme(sg
- .getSequences(viewport.hiddenRepSequences), sg.getWidth());
+ sg.cs = new ClustalxColourScheme(
+ sg.getSequences(viewport.hiddenRepSequences),
+ sg.getWidth());
}
else
{
|| cs instanceof Blosum62ColourScheme)
{
sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
- sg.cs.setConsensus(AAFrequency.calculate(sg
- .getSequences(viewport.hiddenRepSequences), 0, sg
- .getWidth()));
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(viewport.hiddenRepSequences), 0,
+ sg.getWidth()));
}
else
{
if (viewport.getConservationSelected())
{
Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3, sg
- .getSequences(viewport.hiddenRepSequences), 0,
+ ResidueProperties.propHash, 3,
+ sg.getSequences(viewport.hiddenRepSequences), 0,
viewport.alignment.getWidth() - 1);
c.calculate();
c.verdict(false, viewport.ConsPercGaps);
if (viewport.getAbovePIDThreshold()
&& viewport.globalColourScheme != null)
{
- SliderPanel.setPIDSliderSource(alignPanel, viewport
- .getGlobalColourScheme(), "Background");
+ SliderPanel.setPIDSliderSource(alignPanel,
+ viewport.getGlobalColourScheme(), "Background");
SliderPanel.showPIDSlider();
}
}
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByLength(viewport.getAlignment());
- addHistoryItem(new OrderCommand("Length Sort", oldOrder, viewport.alignment));
+ addHistoryItem(new OrderCommand("Length Sort", oldOrder,
+ viewport.alignment));
alignPanel.paintAlignment(true);
}
|| (viewport.getSelectionGroup() == null && viewport.alignment
.getHeight() > 1))
{
- final TreePanel tp = new TreePanel(viewport, type, pwType);
+ final TreePanel tp = new TreePanel(alignPanel, type, pwType);
addTreeMenuItem(tp, title);
public void loadTree(jalview.io.NewickFile tree, String treeFile)
{
- TreePanel tp = new TreePanel(viewport, treeFile, "From File - ", tree);
+ TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
addTreeMenuItem(tp, treeFile);
}
};
});
}
-
+ public boolean sortBy(AlignmentOrder alorder, String undoname)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment()
+ .getSequencesArray();
+ if (viewport.applet.debug)
+ {
+ System.err.println("Sorting "+alorder.getOrder().size()+" in alignment '"+getTitle()+"'");
+ }
+ AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
+ if (undoname!=null)
+ {
+ addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.alignment));
+ }
+ alignPanel.paintAlignment(true);
+ return true;
+ }
protected void documentation_actionPerformed()
{
showURL("http://www.jalview.org/help.html", "HELP");
g.setFont(new Font("Helvetica", Font.BOLD, 12));
g.drawString("Build date: " + builddate, x, y += fh);
g.setFont(new Font("Helvetica", Font.PLAIN, 12));
- g
- .drawString(
- "Authors: Andrew Waterhouse, Jim Procter, Michele Clamp, James Cuff, Steve Searle,",
- x, y += fh * 1.5);
+ g.drawString(
+ "Authors: Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,",
+ x, y += fh * 1.5);
g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);
- g
- .drawString(
- "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
- x, y += fh);
- g
- .drawString(
- "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
- x, y += fh);
+ g.drawString(
+ "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
+ x, y += fh);
+ g.drawString(
+ "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
+ x, y += fh);
g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
- g
- .drawString(
- "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
- x, y += fh);
- g
- .drawString(
- "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
- x, y += fh);
+ g.drawString(
+ "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
+ x, y += fh);
+ g.drawString(
+ "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
+ x, y += fh);
g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
x, y += fh);
}
{
System.out.println("Show url: " + url);
}
- viewport.applet.getAppletContext().showDocument(
- new java.net.URL(url), target);
+ if (url.indexOf("javascript:") == 0)
+ {
+ // no target for the javascript context
+ viewport.applet.getAppletContext().showDocument(
+ new java.net.URL(url));
+ }
+ else
+ {
+ viewport.applet.getAppletContext().showDocument(
+ new java.net.URL(url), target);
+ }
} catch (Exception ex)
{
ex.printStackTrace();
CheckboxMenuItem seqLimits = new CheckboxMenuItem();
CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
-
+
CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
+ Menu autoAnnMenu=new Menu();
+ CheckboxMenuItem showSequenceLogo= new CheckboxMenuItem();
+ CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
+ CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
+ CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
+ CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
private void jbInit() throws Exception
{
hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
hideAllSelection.setLabel("Selected Region");
showAllHidden.setLabel("All Sequences and Columns");
+ showGroupConsensus.setLabel("Group Consensus");
+ showGroupConservation.setLabel("Group Conservation");
+ showConsensusHistogram.setLabel("Show Consensus Histogram");
+ showSequenceLogo.setLabel("Show Consensus Logo");
+ applyAutoAnnotationSettings.setLabel("Apply to all groups");
+ applyAutoAnnotationSettings.setState(true);
+ autoAnnMenu.setLabel("Autocalculated Annotation");
+
invertColSel.addActionListener(this);
showColumns.addActionListener(this);
showSeqs.addActionListener(this);
hideAllButSelection.addActionListener(this);
hideAllSelection.addActionListener(this);
showAllHidden.addActionListener(this);
+ showGroupConsensus.addItemListener(this);
+ showGroupConservation.addItemListener(this);
+ showConsensusHistogram.addItemListener(this);
+ showSequenceLogo.addItemListener(this);
+ applyAutoAnnotationSettings.addItemListener(this);
formatMenu.setLabel("Format");
selectMenu.setLabel("Select");
newView.setLabel("New View");
viewMenu.addSeparator();
viewMenu.add(followMouseOverFlag);
viewMenu.add(annotationPanelMenuItem);
+ autoAnnMenu.add(applyAutoAnnotationSettings);
+ autoAnnMenu.add(showConsensusHistogram);
+ autoAnnMenu.add(showSequenceLogo);
+ autoAnnMenu.addSeparator();
+ autoAnnMenu.add(showGroupConservation);
+ autoAnnMenu.add(showGroupConsensus);
+ viewMenu.add(autoAnnMenu);
viewMenu.addSeparator();
viewMenu.add(sequenceFeatures);
viewMenu.add(featureSettings);
viewport.applet.setLayout(new BorderLayout());
viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
viewport.applet.add(statusBar, BorderLayout.SOUTH);
- alignPanel.setSize(viewport.applet.getSize().width, viewport.applet
- .getSize().height
- - embeddedMenu.HEIGHT - statusBar.HEIGHT);
+ alignPanel.setSize(viewport.applet.getSize().width,
+ viewport.applet.getSize().height - embeddedMenu.HEIGHT
+ - statusBar.HEIGHT);
viewport.applet.add(alignPanel, BorderLayout.CENTER);
+ final AlignFrame me = this;
+ viewport.applet.addFocusListener(new FocusListener()
+ {
+
+ @Override
+ public void focusLost(FocusEvent e)
+ {
+ if (me.viewport.applet.currentAlignFrame==me) {
+ me.viewport.applet.currentAlignFrame = null;
+ }}
+
+ @Override
+ public void focusGained(FocusEvent e)
+ {
+ me.viewport.applet.currentAlignFrame = me;
+ }
+ });
viewport.applet.validate();
}
else
DEFAULT_HEIGHT);
}
}
+
+ /**
+ * create a new binding between structures in an existing jmol viewer instance
+ * and an alignpanel with sequences that have existing PDBFile entries. Note,
+ * this does not open a new Jmol window, or modify the display of the
+ * structures in the original jmol window. Note This method doesn't work
+ * without an additional javascript library to exchange messages between the
+ * distinct applets. See http://issues.jalview.org/browse/JAL-621
+ *
+ * @param viewer
+ * JmolViewer instance
+ * @param sequenceIds
+ * - sequence Ids to search for associations
+ */
+ public SequenceStructureBinding addStructureViewInstance(
+ Object jmolviewer, String[] sequenceIds)
+ {
+ org.jmol.api.JmolViewer viewer = null;
+ try
+ {
+ viewer = (org.jmol.api.JmolViewer) jmolviewer;
+ } catch (ClassCastException ex)
+ {
+ System.err.println("Unsupported viewer object :"
+ + jmolviewer.getClass());
+ }
+ if (viewer == null)
+ {
+ System.err.println("Can't use this object as a structure viewer:"
+ + jmolviewer.getClass());
+ return null;
+ }
+ SequenceI[] seqs = null;
+ if (sequenceIds == null || sequenceIds.length == 0)
+ {
+ seqs = viewport.getAlignment().getSequencesArray();
+ }
+ else
+ {
+ Vector sqi = new Vector();
+ AlignmentI al = viewport.getAlignment();
+ for (int sid = 0; sid < sequenceIds.length; sid++)
+ {
+ SequenceI sq = al.findName(sequenceIds[sid]);
+ if (sq != null)
+ {
+ sqi.addElement(sq);
+ }
+ }
+ if (sqi.size() > 0)
+ {
+ seqs = new SequenceI[sqi.size()];
+ for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
+ {
+ seqs[sid] = (SequenceI) sqi.elementAt(sid);
+ }
+ }
+ else
+ {
+ return null;
+ }
+ }
+ ExtJmol jmv = null;
+ // TODO: search for a jmv that involves viewer
+ if (jmv == null)
+ { // create a new viewer/jalview binding.
+ jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] {seqs});
+ }
+ return jmv;
+
+ }
+
+ public boolean addPdbFile(String sequenceId, String pdbEntryString,
+ String pdbFile)
+ {
+ SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
+ boolean needtoadd = false;
+ if (toaddpdb != null)
+ {
+ Vector pdbe = toaddpdb.getPDBId();
+ PDBEntry pdbentry = null;
+ if (pdbe != null && pdbe.size() > 0)
+ {
+ for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
+ {
+ pdbentry = (PDBEntry) pdbe.elementAt(pe);
+ if (!pdbentry.getId().equals(pdbEntryString)
+ && !pdbentry.getFile().equals(pdbFile))
+ {
+ pdbentry = null;
+ }
+ else
+ {
+ continue;
+ }
+ }
+ }
+ if (pdbentry == null)
+ {
+ pdbentry = new PDBEntry();
+ pdbentry.setId(pdbEntryString);
+ pdbentry.setFile(pdbFile);
+ needtoadd = true; // add this new entry to sequence.
+ }
+ // resolve data source
+ // TODO: this code should be a refactored to an io package
+ String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
+ if (protocol == null)
+ {
+ return false;
+ }
+ if (needtoadd)
+ {
+ // make a note of the access mode and add
+ if (pdbentry.getProperty() == null)
+ {
+ pdbentry.setProperty(new Hashtable());
+ }
+ pdbentry.getProperty().put("protocol", protocol);
+ toaddpdb.addPDBId(pdbentry);
+ }
+ }
+ return true;
+ }
+
+ private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
+ {
+ if (seqs != null)
+ {
+ Vector sequences = new Vector();
+ for (int i = 0; i < seqs.length; i++)
+ {
+ if (seqs[i] != null)
+ {
+ sequences.addElement(new Object[]
+ { seqs[i], (chains != null) ? chains[i] : null });
+ }
+ }
+ seqs = new SequenceI[sequences.size()];
+ chains = new String[sequences.size()];
+ for (int i = 0, isize = sequences.size(); i < isize; i++)
+ {
+ Object[] oj = (Object[]) sequences.elementAt(i);
+
+ seqs[i] = (SequenceI) oj[0];
+ chains[i] = (String) oj[1];
+ }
+ }
+ return new Object[]
+ { seqs, chains };
+
+ }
+
+ public void newStructureView(JalviewLite applet, PDBEntry pdb,
+ SequenceI[] seqs, String[] chains, String protocol)
+ {
+ // Scrub any null sequences from the array
+ Object[] sqch = cleanSeqChainArrays(seqs, chains);
+ seqs = (SequenceI[]) sqch[0];
+ chains = (String[]) sqch[1];
+ if (seqs == null || seqs.length == 0)
+ {
+ System.err
+ .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
+ }
+ if (protocol == null || protocol.trim().length() == 0
+ || protocol.equals("null"))
+ {
+ protocol = (String) pdb.getProperty().get("protocol");
+ if (protocol == null)
+ {
+ System.err.println("Couldn't work out protocol to open structure: "
+ + pdb.getId());
+ return;
+ }
+ }
+ if (applet.isAlignPdbStructures() && applet.jmolAvailable)
+ {
+ // can only do alignments with Jmol
+ // find the last jmol window assigned to this alignment
+ jalview.appletgui.AppletJmol ajm = null, tajm;
+ Vector jmols = applet
+ .getAppletWindow(jalview.appletgui.AppletJmol.class);
+ for (int i = 0, iSize = jmols.size(); i < iSize; i++)
+ {
+ tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
+ if (tajm.ap.alignFrame == this)
+ {
+ ajm = tajm;
+ break;
+ }
+ }
+ if (ajm != null)
+ {
+ 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 jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
+ protocol);
+ applet.lastFrameX += 40;
+ applet.lastFrameY += 40;
+ }
+ else
+ {
+ new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
+ }
+
+ }
+
+ public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
+ SequenceI[][] seqs, String[][] chains, String[] protocols)
+ {
+ // TODO Auto-generated method stub
+ System.err.println("Aligned Structure View: Not yet implemented.");
+ }
+
+ /**
+ * modify the current selection, providing the user has not made a selection already.
+ * @param sel - sequences from this alignment
+ * @param csel - columns to be selected on the alignment
+ */
+ public void select(SequenceGroup sel, ColumnSelection csel)
+ {
+ alignPanel.seqPanel.selection(sel, csel, null);
+ }
}
git://source.jalview.org / jalview.git / blobdiff