/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
package jalview.appletgui;
import java.net.*;
import java.util.*;
+import java.applet.Applet;
import java.awt.*;
import java.awt.event.*;
+import org.jmol.api.JmolViewer;
+
import jalview.analysis.*;
+import jalview.api.SequenceStructureBinding;
import jalview.bin.JalviewLite;
import jalview.commands.*;
import jalview.datamodel.*;
{
sortPairwiseMenuItem_actionPerformed();
}
+ else if (param.equalsIgnoreCase("Length"))
+ {
+ sortLengthMenuItem_actionPerformed();
+ }
}
param = applet.getParameter("wrap");
* DOCUMENT ME!
*
* @param String
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void parseFeaturesFile(String file, String type)
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);
} catch (Exception ex)
{
ex.printStackTrace();
}
viewport.showSequenceFeatures = true;
sequenceFeatures.setState(true);
- if (viewport.featureSettings!=null)
+ if (viewport.featureSettings != null)
{
viewport.featureSettings.refreshTable();
}
}
alignPanel.paintAlignment(true);
}
+
/**
* called by key handler and the hide all/show all menu items
+ *
* @param toggleSeqs
* @param toggleCols
*/
- private void toggleHiddenRegions(boolean toggleSeqs,
- boolean toggleCols)
+ private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
{
boolean hide = false;
SequenceGroup sg = viewport.getSelectionGroup();
// 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.colSel != null
- && viewport.colSel.getSelected() != null && viewport.colSel
+ if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
.getSelected().size() > 0)
|| (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
.getEndRes()))
}
}
}
+
public void keyReleased(KeyEvent evt)
{
}
else if (evt.getSource() == this.centreColumnLabelFlag)
{
centreColumnLabelFlag_stateChanged();
- } else if (evt.getSource() == this.followMouseOverFlag)
+ }
+ else if (evt.getSource() == this.followMouseOverFlag)
{
mouseOverFlag_stateChanged();
}
private void mouseOverFlag_stateChanged()
{
viewport.followHighlight = followMouseOverFlag.getState();
- // TODO: could kick the scrollTo mechanism to reset view for current searchresults.
+ // TODO: could kick the scrollTo mechanism to reset view for current
+ // searchresults.
}
private void centreColumnLabelFlag_stateChanged()
viewport.hideAllSelectedSeqs();
alignPanel.paintAlignment(true);
}
- else if (source == hideAllButSelection) {
- toggleHiddenRegions(false,false);
+ else if (source == hideAllButSelection)
+ {
+ toggleHiddenRegions(false, false);
alignPanel.paintAlignment(true);
}
- else if (source == hideAllSelection) {
+ else if (source == hideAllSelection)
+ {
SequenceGroup sg = viewport.getSelectionGroup();
viewport.expandColSelection(sg, false);
viewport.hideAllSelectedSeqs();
viewport.hideSelectedColumns();
alignPanel.paintAlignment(true);
}
- else if (source == showAllHidden) {
+ else if (source == showAllHidden)
+ {
viewport.showAllHiddenColumns();
viewport.showAllHiddenSeqs();
alignPanel.paintAlignment(true);
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)
{
{
sortIDMenuItem_actionPerformed();
}
+ else if (source == sortLengthMenuItem)
+ {
+ sortLengthMenuItem_actionPerformed();
+ }
else if (source == sortGroupMenuItem)
{
sortGroupMenuItem_actionPerformed();
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));
}
private Hashtable getDisplayedFeatureCols()
{
- if (alignPanel.getFeatureRenderer()!=null) {
+ if (alignPanel.getFeatureRenderer() != null)
+ {
FeatureRenderer fr = alignPanel.getFeatureRenderer();
Hashtable fcols = new Hashtable();
Enumeration en = viewport.featuresDisplayed.keys();
while (en.hasMoreElements())
{
Object col = en.nextElement();
- fcols.put(col,fr.featureColours.get(col));
+ fcols.put(col, fr.featureColours.get(col));
}
return fcols;
}
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)
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void undoMenuItem_actionPerformed()
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void redoMenuItem_actionPerformed()
{
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);
}
}
+
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(
alignPanel.paintAlignment(true);
}
}
+
protected void deleteGroups_actionPerformed()
{
viewport.alignment.deleteAllGroups();
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
}
+
public void invertColSel_actionPerformed()
{
viewport.invertColumnSelection();
{
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());
* get sequence feature groups that are hidden or shown
*
* @param visible
- * true is visible
+ * true is visible
* @return list
*/
public String[] getFeatureGroupsOfState(boolean visible)
* Change the display state for the given feature groups
*
* @param groups
- * list of group strings
+ * list of group strings
* @param state
- * visible or invisible
+ * visible or invisible
*/
public void setFeatureGroupState(String[] groups, boolean state)
{
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();
}
}
modifyPID_actionPerformed();
}
+
public void sortPairwiseMenuItem_actionPerformed()
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByID(viewport.getAlignment());
- addHistoryItem(new OrderCommand("ID Sort", oldOrder,
+ addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
+ alignPanel.paintAlignment(true);
+ }
+
+ public void sortLengthMenuItem_actionPerformed()
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByLength(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("Length Sort", oldOrder,
viewport.alignment));
alignPanel.paintAlignment(true);
}
public void PCAMenuItem_actionPerformed()
{
// are the sequences aligned?
- if (!viewport.alignment.isAligned())
+ if (!viewport.alignment.isAligned(false))
{
SequenceI current;
int Width = viewport.getAlignment().getWidth();
void NewTreePanel(String type, String pwType, String title)
{
// are the sequences aligned?
- if (!viewport.alignment.isAligned())
+ if (!viewport.alignment.isAligned(false))
{
SequenceI current;
int Width = viewport.getAlignment().getWidth();
jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
addTreeMenuItem(tp, treeFile);
}
+
/**
* sort the alignment using the given treePanel
- * @param treePanel tree used to sort view
- * @param title string used for undo event name
+ *
+ * @param treePanel
+ * tree used to sort view
+ * @param title
+ * string used for undo event name
*/
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("Order by "+title, oldOrder,
+ addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
viewport.alignment));
alignPanel.paintAlignment(true);
}
+
/**
- * Do any automatic reordering of the alignment and add the necessary bits to the menu structure for the new tree
+ * Do any automatic reordering of the alignment and add the necessary bits to
+ * the menu structure for the new tree
+ *
* @param treePanel
* @param title
*/
- protected void addTreeMenuItem(final TreePanel treePanel, final String title)
+ protected void addTreeMenuItem(final TreePanel treePanel,
+ final String title)
{
final MenuItem item = new MenuItem(title);
sortByTreeMenu.add(item);
class AboutPanel extends Canvas
{
String version;
+
String builddate;
+
public AboutPanel(String version, String builddate)
{
this.version = version;
g.setFont(new Font("Helvetica", Font.BOLD, 14));
g.drawString("JalviewLite - Release " + version, x, y += fh);
g.setFont(new Font("Helvetica", Font.BOLD, 12));
- g.drawString("Build date: "+builddate, x, y += fh);
+ 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: Andrew Waterhouse, Jim Procter, 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("Bioinformatics doi: 10.1093/bioinformatics/btp033",x,y+=fh);
+ "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);
}
}
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, "Jalview", 580, 220);
}
{
try
{
- if (url.indexOf(":")==-1)
+ if (url.indexOf(":") == -1)
{
- // TODO: verify (Bas Vroling bug) prepend codebase or server URL to form valid URL
- if (url.indexOf("/")==0)
+ // TODO: verify (Bas Vroling bug) prepend codebase or server URL to
+ // form valid URL
+ if (url.indexOf("/") == 0)
{
String codebase = viewport.applet.getCodeBase().toString();
- url = codebase.substring(0,codebase.length()-viewport.applet.getCodeBase().getFile().length())+url;
- } else {
- url = viewport.applet.getCodeBase()+url;
+ url = codebase.substring(0, codebase.length()
+ - viewport.applet.getCodeBase().getFile().length())
+ + url;
+ }
+ else
+ {
+ url = viewport.applet.getCodeBase() + url;
}
System.out.println("Show url (prepended codebase): " + url);
- } else {
+ }
+ else
+ {
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();
MenuItem sortIDMenuItem = new MenuItem();
+ MenuItem sortLengthMenuItem = new MenuItem();
+
MenuItem sortGroupMenuItem = new MenuItem();
MenuItem removeRedundancyMenuItem = new MenuItem();
MenuItem deleteGroups = new MenuItem();
- MenuItem grpsFromSelection= new MenuItem();
+ MenuItem grpsFromSelection = new MenuItem();
MenuItem delete = new MenuItem();
sortPairwiseMenuItem.addActionListener(this);
sortIDMenuItem.setLabel("by ID");
sortIDMenuItem.addActionListener(this);
+ sortLengthMenuItem.setLabel("by Length");
+ sortLengthMenuItem.addActionListener(this);
sortGroupMenuItem.setLabel("by Group");
sortGroupMenuItem.addActionListener(this);
removeRedundancyMenuItem.setLabel("Remove Redundancy...");
annotationPanelMenuItem.addItemListener(this);
colourTextMenuItem.setLabel("Colour Text");
colourTextMenuItem.addItemListener(this);
- displayNonconservedMenuItem.setLabel("Show non-conserved");
+ displayNonconservedMenuItem.setLabel("Show nonconserved");
displayNonconservedMenuItem.addItemListener(this);
alProperties.addActionListener(this);
overviewMenuItem.setLabel("Overview Window");
pasteMenu.add(pasteNew);
pasteMenu.add(pasteThis);
sort.add(sortIDMenuItem);
+ sort.add(sortLengthMenuItem);
sort.add(sortByTreeMenu);
sort.add(sortGroupMenuItem);
sort.add(sortPairwiseMenuItem);
selectMenu.add(invertColSel);
selectMenu.add(grpsFromSelection);
selectMenu.add(deleteGroups);
-
+
}
MenuItem featureSettings = new MenuItem();
MenuItem hideSequences = new MenuItem();
MenuItem hideAllButSelection = new MenuItem();
+
MenuItem hideAllSelection = new MenuItem();
+
MenuItem showAllHidden = new MenuItem();
Menu formatMenu = new Menu();
* platform independent manner to avoid OSX/Mac menu appendage daftness.
*
* @param reallyEmbedded
- * true to attach the view to the applet area on the page
- * rather than in a new window
+ * true to attach the view to the applet area on the page rather than
+ * in a new window
*/
public void createAlignFrameWindow(boolean reallyEmbedded, String title)
{
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);
viewport.applet.validate();
}
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
+ *
+ * @param viewer
+ * JmolViewer instance
+ * @param sequenceIds
+ * - sequence Ids to search for associations
+ * This method doesn't work. See http://issues.jalview.org/browse/JAL-621
+ *
+ 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, 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.");
+ }
}
git://source.jalview.org / jalview.git / blobdiff