import jalview.appletgui.SequenceRenderer;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
import jalview.io.StructureFile;
import jalview.structure.AtomSpec;
import jalview.structure.StructureListener;
StructureSelectionManager ssm;
public AppletPDBCanvas(PDBEntry pdbentry, SequenceI[] seq,
- String[] chains, AlignmentPanel ap, String protocol)
+ String[] chains, AlignmentPanel ap, DataSourceType protocol)
{
this.ap = ap;
try
{
- pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol);
+ pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol, null);
- if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+ if (protocol == DataSourceType.PASTE)
{
pdbentry.setFile("INLINE" + pdb.getId());
}
for (int i = 0; i < pdb.getChains().size(); i++)
{
- mappingDetails.append("\n\nPDB Sequence is :\nSequence = "
- + pdb.getChains().elementAt(i).sequence.getSequenceAsString());
+ mappingDetails
+ .append("\n\nPDB Sequence is :\nSequence = "
+ + pdb.getChains().elementAt(i).sequence
+ .getSequenceAsString());
mappingDetails.append("\nNo of residues = "
+ pdb.getChains().elementAt(i).residues.size() + "\n\n");
// Align the sequence to the pdb
// TODO: DNa/Pep switch
AlignSeq as = new AlignSeq(sequence,
- pdb.getChains().elementAt(i).sequence,
- pdb.getChains().elementAt(i).isNa ? AlignSeq.DNA : AlignSeq.PEP);
+ pdb.getChains().elementAt(i).sequence, pdb.getChains()
+ .elementAt(i).isNa ? AlignSeq.DNA : AlignSeq.PEP);
as.calcScoreMatrix();
as.traceAlignment();
PrintStream ps = new PrintStream(System.out)
import jalview.gui.AlignmentPanel;
import jalview.gui.FeatureRenderer;
import jalview.gui.SequenceRenderer;
+import jalview.io.DataSourceType;
import jalview.io.StructureFile;
import jalview.structure.AtomSpec;
import jalview.structure.StructureListener;
String errorMessage;
void init(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
- AlignmentPanel ap, String protocol)
+ AlignmentPanel ap, DataSourceType protocol)
{
this.ap = ap;
this.pdbentry = pdbentry;
try
{
- pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol);
+ pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol,
+ ap.alignFrame);
- if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+ if (protocol.equals(jalview.io.DataSourceType.PASTE))
{
pdbentry.setFile("INLINE" + pdb.getId());
}
for (int i = 0; i < pdb.getChains().size(); i++)
{
- mappingDetails.append("\n\nPDB Sequence is :\nSequence = "
- + pdb.getChains().elementAt(i).sequence.getSequenceAsString());
+ mappingDetails
+ .append("\n\nPDB Sequence is :\nSequence = "
+ + pdb.getChains().elementAt(i).sequence
+ .getSequenceAsString());
mappingDetails.append("\nNo of residues = "
+ pdb.getChains().elementAt(i).residues.size() + "\n\n");
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.api.AlignViewportI;
+import jalview.api.FeatureColourI;
import jalview.api.FeatureRenderer;
import jalview.api.FeatureSettingsControllerI;
import jalview.api.SequenceStructureBinding;
import jalview.datamodel.SequenceI;
import jalview.io.AnnotationFile;
import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
import jalview.io.FeaturesFile;
+import jalview.io.FileFormat;
import jalview.io.TCoffeeScoreFile;
import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.BuriedColourScheme;
import java.util.Arrays;
import java.util.Deque;
import java.util.HashMap;
-import java.util.Hashtable;
import java.util.List;
import java.util.Map;
import java.util.StringTokenizer;
{
viewport.setColumnSelection(columnSelection);
}
+ viewport.setScaleAboveWrapped(scaleAbove.getState());
alignPanel = new AlignmentPanel(this, viewport);
avc = new jalview.controller.AlignViewController(this, viewport,
* is protocol for accessing data referred to by file
*/
- public boolean parseFeaturesFile(String file, String type)
+ public boolean parseFeaturesFile(String file, DataSourceType type)
{
return parseFeaturesFile(file, type, true);
}
*
* @param file
* file URL, content, or other resolvable path
- * @param type
+ * @param sourceType
* is protocol for accessing data referred to by file
* @param autoenabledisplay
* when true, display features flag will be automatically enabled if
* features are loaded
* @return true if data parsed as a features file
*/
- public boolean parseFeaturesFile(String file, String type,
+ public boolean parseFeaturesFile(String file, DataSourceType sourceType,
boolean autoenabledisplay)
{
boolean featuresFile = false;
try
{
- Map<String, Object> colours = alignPanel.seqPanel.seqCanvas
+ Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
.getFeatureRenderer().getFeatureColours();
boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
"relaxedidmatch", false);
- featuresFile = new FeaturesFile(file, type).parse(
+ featuresFile = new FeaturesFile(file, sourceType).parse(
viewport.getAlignment(), colours, true, relaxedIdMatching);
} catch (Exception ex)
{
// 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.getColumnSelection() != null
- && viewport.getColumnSelection().getSelected() != null && viewport
- .getColumnSelection().getSelected().size() > 0)
+ if (viewport.hasSelectedColumns()
|| (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
.getEndRes()))
{
hide = true;
viewport.hideAllSelectedSeqs();
}
- else if (!(toggleCols && viewport.getColumnSelection().getSelected()
- .size() > 0))
+ else if (!(toggleCols && viewport.hasSelectedColumns()))
{
viewport.showAllHiddenSeqs();
}
if (toggleCols)
{
- if (viewport.getColumnSelection().getSelected().size() > 0)
+ if (viewport.hasSelectedColumns())
{
viewport.hideSelectedColumns();
if (!toggleSeqs)
if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
{
for (AlignmentAnnotation aa : alignPanel.getAlignment()
- .getAlignmentAnnotation())
- {
- boolean visible = (aa.sequenceRef == null ? showForAlignment
- : showForSequences);
- aa.visible = visible;
+ .getAlignmentAnnotation())
+ {
+ boolean visible = (aa.sequenceRef == null ? showForAlignment
+ : showForSequences);
+ aa.visible = visible;
}
}
alignPanel.validateAnnotationDimensions(true);
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+ JalviewLite.addFrame(frame, MessageManager.formatMessage(
"label.alignment_output_command",
new Object[] { e.getActionCommand() }), 600, 500);
- FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
+ FileFormat fileFormat = FileFormat.valueOf(e.getActionCommand());
cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
- e.getActionCommand(), viewport.getAlignment(),
+ fileFormat, viewport.getAlignment(),
viewport.getShowJVSuffix()));
}
return annotation;
}
- private Map<String, Object> getDisplayedFeatureCols()
+ private Map<String, FeatureColourI> getDisplayedFeatureCols()
{
if (alignPanel.getFeatureRenderer() != null
&& viewport.getFeaturesDisplayed() != null)
FeaturesFile formatter = new FeaturesFile();
if (format.equalsIgnoreCase("Jalview"))
{
- features = formatter.printJalviewFormat(viewport
- .getAlignment().getSequencesArray(),
- getDisplayedFeatureCols());
+ features = formatter.printJalviewFormat(viewport.getAlignment()
+ .getSequencesArray(), getDisplayedFeatureCols());
}
else
{
url.append(appendProtocol(viewport.applet.getParameter("annotations")));
}
- if (viewport.applet.getParameter("jnetfile") != null)
+ if (viewport.applet.getParameter("jnetfile") != null
+ || viewport.applet.getParameter("jpredfile") != null)
{
url.append("&annotations=");
- url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
+ url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet
+ .getParameter("jnetfile") : viewport.applet
+ .getParameter("jpredfile")));
}
if (viewport.applet.getParameter("defaultColour") != null)
}
sg.setEndRes(viewport.getAlignment().getWidth() - 1);
viewport.setSelectionGroup(sg);
- alignPanel.paintAlignment(true);
+ // JAL-2034 - should delegate to
+ // alignPanel to decide if overview needs
+ // updating.
+ alignPanel.paintAlignment(false);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
viewport.setSelectionGroup(null);
alignPanel.idPanel.idCanvas.searchResults = null;
alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
- alignPanel.paintAlignment(true);
+ // JAL-2034 - should delegate to
+ // alignPanel to decide if overview needs
+ // updating.
+ alignPanel.paintAlignment(false);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
inputText.addActionListener(this);
Menu outputTextboxMenu = new Menu(
MessageManager.getString("label.out_to_textbox"));
- for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
+ for (String ff : FileFormat.getWritableFormats(true))
{
-
- MenuItem item = new MenuItem(
- jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
+ MenuItem item = new MenuItem(ff);
item.addActionListener(new java.awt.event.ActionListener()
{
nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
nucleotideColour.addActionListener(this);
modifyPID.setLabel(MessageManager
- .getString("label.modify_identity_thereshold"));
+ .getString("label.modify_identity_threshold"));
modifyPID.addActionListener(this);
modifyConservation.setLabel(MessageManager
- .getString("label.modify_conservation_thereshold"));
+ .getString("label.modify_conservation_threshold"));
modifyConservation.addActionListener(this);
annotationColour.setLabel(MessageManager
.getString("action.by_annotation"));
}
// resolve data source
// TODO: this code should be a refactored to an io package
- String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
+ DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
+ pdbFile, FileFormat.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);
+ pdbentry.setProperty("protocol", protocol);
toaddpdb.addPDBId(pdbentry);
alignPanel.getStructureSelectionManager()
.registerPDBEntry(pdbentry);
}
public void newStructureView(JalviewLite applet, PDBEntry pdb,
- SequenceI[] seqs, String[] chains, String protocol)
+ SequenceI[] seqs, String[] chains, DataSourceType protocol)
{
// Scrub any null sequences from the array
Object[] sqch = cleanSeqChainArrays(seqs, chains);
System.err
.println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
}
- if (protocol == null || protocol.trim().length() == 0
- || protocol.equals("null"))
+ if (protocol == null)
{
- protocol = (String) pdb.getProperty().get("protocol");
+ String sourceType = (String) pdb.getProperty("protocol");
+ try
+ {
+ protocol = DataSourceType.valueOf(sourceType);
+ } catch (IllegalArgumentException e)
+ {
+ // ignore
+ }
if (protocol == null)
{
System.err.println("Couldn't work out protocol to open structure: "
{
// register the association(s) and quit, don't create any windows.
if (StructureSelectionManager.getStructureSelectionManager(applet)
- .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
+ .setMapping(seqs, chains, pdb.getFile(), protocol, null) == null)
{
System.err.println("Failed to map " + pdb.getFile() + " ("
+ protocol + ") to any sequences");
{
// 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);
+ AppletJmol ajm = null, tajm;
+ Vector jmols = applet.getAppletWindow(AppletJmol.class);
for (int i = 0, iSize = jmols.size(); i < iSize; i++)
{
- tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
+ tajm = (AppletJmol) jmols.elementAt(i);
if (tajm.ap.alignFrame == this)
{
ajm = tajm;
// otherwise, create a new window
if (applet.jmolAvailable)
{
- new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
+ new AppletJmol(pdb, seqs, chains, alignPanel,
protocol);
applet.lastFrameX += 40;
applet.lastFrameY += 40;
*/
package jalview.appletgui;
+import jalview.bin.JalviewLite;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
import jalview.io.FileParse;
+import jalview.io.DataSourceType;
import jalview.io.StructureFile;
import jalview.schemes.BuriedColourScheme;
import jalview.schemes.HelixColourScheme;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.util.ArrayList;
-import java.util.Hashtable;
import java.util.List;
import java.util.Vector;
}
public AppletJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
- AlignmentPanel ap, String protocol)
+ AlignmentPanel ap, DataSourceType protocol)
{
this.ap = ap;
jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(),
new PDBEntry[] { pdbentry }, new SequenceI[][] { seq },
- new String[][] { chains }, protocol);
+ protocol);
jmb.setColourBySequence(true);
if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
{
- if (protocol.equals(AppletFormatAdapter.PASTE))
+ if (protocol == DataSourceType.PASTE)
{
pdbentry.setId("PASTED PDB"
+ (chains == null ? "_" : chains.toString()));
}
}
- if (jalview.bin.JalviewLite.debug)
+ if (JalviewLite.debug)
{
System.err
.println("AppletJmol: PDB ID is '" + pdbentry.getId() + "'");
{
reader = StructureSelectionManager.getStructureSelectionManager(
ap.av.applet).setMapping(seq, chains, pdbentry.getFile(),
- protocol);
+ protocol, null);
// PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW?
// FOR NOW, LETS JUST OPEN A NEW WINDOW
}
closeViewer();
}
});
- if (pdbentry.getProperty() == null)
- {
- pdbentry.setProperty(new Hashtable());
- pdbentry.getProperty().put("protocol", protocol);
- }
+ pdbentry.setProperty("protocol", protocol);
if (pdbentry.getFile() != null)
+
{
// import structure data from pdbentry.getFile based on given protocol
- if (protocol.equals(AppletFormatAdapter.PASTE))
+ if (protocol == DataSourceType.PASTE)
{
// TODO: JAL-623 : correctly record file contents for matching up later
// pdbentry.getProperty().put("pdbfilehash",""+pdbentry.getFile().hashCode());
loadInline(pdbentry.getFile());
}
- else if (protocol.equals(AppletFormatAdapter.FILE)
- || protocol.equals(AppletFormatAdapter.URL))
+ else if (protocol == DataSourceType.FILE
+ || protocol == DataSourceType.URL)
{
jmb.viewer.openFile(pdbentry.getFile());
}
jmb.loadInline(string);
}
- void setChainMenuItems(Vector<String> chains)
+ void setChainMenuItems(List<String> chains)
{
chainMenu.removeAll();
repaint();
return;
}
- setChainMenuItems(jmb.chainNames);
+ setChainMenuItems(jmb.getChainNames());
jmb.colourBySequence(ap);
setTitle(jmb.getViewerTitle());
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JalviewJmolBinding;
+ import jalview.gui.IProgressIndicator;
+import jalview.io.DataSourceType;
import jalview.structure.StructureSelectionManager;
import java.awt.Container;
import java.util.Map;
-import javajs.awt.Dimension;
-
import org.jmol.api.JmolAppConsoleInterface;
import org.jmol.console.AppletConsole;
import org.jmol.java.BS;
public AppletJmolBinding(AppletJmol appletJmol,
StructureSelectionManager sSm, PDBEntry[] pdbentry,
- SequenceI[][] seq, String[][] chains, String protocol)
+ SequenceI[][] seq, DataSourceType protocol)
{
- super(sSm, pdbentry, seq, chains, protocol);
+ super(sSm, pdbentry, seq, protocol);
appletJmolBinding = appletJmol;
}
}
@Override
- public Dimension resizeInnerPanel(String data)
+ public int[] resizeInnerPanel(String data)
{
// TODO Auto-generated method stub
return null;
// TODO Auto-generated method stub
return null;
}
+
+ @Override
+ protected IProgressIndicator getIProgressIndicator()
+ {
+ // no progress indicators on the applet
+ return null;
+ }
}
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JalviewJmolBinding;
+ import jalview.gui.IProgressIndicator;
+import jalview.io.DataSourceType;
import java.awt.Container;
import java.util.ArrayList;
private AlignmentPanel ap;
- protected ExtJmol(jalview.appletgui.AlignFrame alframe,
- PDBEntry[] pdbentry, SequenceI[][] seq, String[][] chains,
- String protocol)
+ protected ExtJmol(AlignFrame alframe,
+ PDBEntry[] pdbentry, SequenceI[][] seq,
+ DataSourceType protocol)
{
super(alframe.alignPanel.getStructureSelectionManager(), pdbentry, seq,
- chains, protocol);
+ protocol);
}
public ExtJmol(Viewer viewer, AlignmentPanel alignPanel,
}
@Override
+ protected IProgressIndicator getIProgressIndicator()
+ {
+ // no progress indicators on applet (could access javascript for this)
+ return null;
+ }
+
+ @Override
public void updateColours(Object source)
{
}
}
+
@Override
public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
{
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+ import jalview.gui.IProgressIndicator;
-import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
import jalview.io.StructureFile;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
import java.io.File;
import java.net.URL;
import java.security.AccessControlException;
+import java.util.ArrayList;
import java.util.Hashtable;
import java.util.List;
import java.util.Map;
import java.util.Vector;
-import javajs.awt.Dimension;
-
import org.jmol.adapter.smarter.SmarterJmolAdapter;
import org.jmol.api.JmolAppConsoleInterface;
import org.jmol.api.JmolSelectionListener;
import org.jmol.api.JmolViewer;
import org.jmol.c.CBK;
import org.jmol.script.T;
-import org.jmol.viewer.JC;
import org.jmol.viewer.Viewer;
public abstract class JalviewJmolBinding extends AAStructureBindingModel
Vector<String> atomsPicked = new Vector<String>();
- public Vector<String> chainNames;
+ private List<String> chainNames;
Hashtable<String, String> chainFile;
boolean loadedInline;
- /**
- * current set of model filenames loaded in the Jmol instance
- */
- String[] modelFileNames = null;
-
StringBuffer resetLastRes = new StringBuffer();
public Viewer viewer;
public JalviewJmolBinding(StructureSelectionManager ssm,
- PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
- String protocol)
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
+ DataSourceType protocol)
{
- super(ssm, pdbentry, sequenceIs, chains, protocol);
+ super(ssm, pdbentry, sequenceIs, protocol);
/*
* viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(),
* "jalviewJmol", ap.av.applet .getDocumentBase(),
public void closeViewer()
{
- viewer.acm.setModeMouse(JC.MOUSE_NONE);
// remove listeners for all structures in viewer
getSsm().removeStructureViewerListener(this, this.getPdbFile());
- // and shut down jmol
- viewer.evalStringQuiet("zap");
- viewer.setJmolStatusListener(null);
+ viewer.dispose();
lastCommand = null;
viewer = null;
releaseUIResources();
} catch (InterruptedException i)
{
}
- ;
}
+
+ /*
+ * get the distinct structure files modelled
+ * (a file with multiple chains may map to multiple sequences)
+ */
String[] files = getPdbFile();
if (!waitForFileLoad(files))
{
* 'matched' array will hold 'true' for visible alignment columns where
* all sequences have a residue with a mapping to the PDB structure
*/
+ // TODO could use a BitSet for matched
boolean matched[] = new boolean[alignment.getWidth()];
for (int m = 0; m < matched.length; m++)
{
* generate select statements to select regions to superimpose structures
*/
{
+ // TODO extract method to construct selection statements
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
String chainCd = ":" + structures[pdbfnum].chain;
}
}
StringBuilder command = new StringBuilder(256);
+ // command.append("set spinFps 10;\n");
+
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
if (pdbfnum == refStructure || selcom[pdbfnum] == null
}
if (selectioncom.length() > 0)
{
- System.out.println("Select regions:\n" + selectioncom.toString());
+ // TODO is performing selectioncom redundant here? is done later on
+ // System.out.println("Select regions:\n" + selectioncom.toString());
evalStateCommand("select *; cartoons off; backbone; select ("
+ selectioncom.toString() + "); cartoons; ");
// selcom.append("; ribbons; ");
String cmdString = command.toString();
- System.out.println("Superimpose command(s):\n" + cmdString);
+ // System.out.println("Superimpose command(s):\n" + cmdString);
evalStateCommand(cmdString);
}
{
selectioncom.setLength(selectioncom.length() - 1);
}
- System.out.println("Select regions:\n" + selectioncom.toString());
+ // System.out.println("Select regions:\n" + selectioncom.toString());
evalStateCommand("select *; cartoons off; backbone; select ("
+ selectioncom.toString() + "); cartoons; ");
// evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString());
}
if (modelFileNames == null)
{
- String mset[] = new String[viewer.ms.mc];
- _modelFileNameMap = new int[mset.length];
+ List<String> mset = new ArrayList<String>();
+ _modelFileNameMap = new int[viewer.ms.mc];
String m = viewer.ms.getModelFileName(0);
if (m != null)
{
- mset[0] = m;
+ String filePath = m;
try
{
- mset[0] = new File(m).getAbsolutePath();
+ filePath = new File(m).getAbsolutePath();
} catch (AccessControlException x)
{
// usually not allowed to do this in applet
.println("jmolBinding: Using local file string from Jmol: "
+ m);
}
- if (mset[0].indexOf("/file:") != -1)
+ if (filePath.indexOf("/file:") != -1)
{
// applet path with docroot - discard as format won't match pdbfile
- mset[0] = m;
+ filePath = m;
}
+ mset.add(filePath);
_modelFileNameMap[0] = 0; // filename index for first model is always 0.
}
int j = 1;
- for (int i = 1; i < mset.length; i++)
+ for (int i = 1; i < viewer.ms.mc; i++)
{
m = viewer.ms.getModelFileName(i);
- mset[j] = m;
+ String filePath = m;
if (m != null)
{
try
{
- mset[j] = new File(m).getAbsolutePath();
+ filePath = new File(m).getAbsolutePath();
} catch (AccessControlException x)
{
// usually not allowed to do this in applet, so keep raw handle
// System.err.println("jmolBinding: Using local file string from Jmol: "+m);
}
}
- _modelFileNameMap[j] = i; // record the model index for the filename
- // skip any additional models in the same file (NMR structures)
- if ((mset[j] == null ? mset[j] != mset[j - 1]
- : (mset[j - 1] == null || !mset[j].equals(mset[j - 1]))))
+
+ /*
+ * add this model unless it is read from a structure file we have
+ * already seen (example: 2MJW is an NMR structure with 10 models)
+ */
+ if (!mset.contains(filePath))
{
+ mset.add(filePath);
+ _modelFileNameMap[j] = i; // record the model index for the filename
j++;
}
}
- modelFileNames = new String[j];
- System.arraycopy(mset, 0, modelFileNames, 0, j);
+ modelFileNames = mset.toArray(new String[mset.size()]);
}
return modelFileNames;
}
fileLoadingError = null;
String[] oldmodels = modelFileNames;
modelFileNames = null;
- chainNames = new Vector<String>();
+ chainNames = new ArrayList<String>();
chainFile = new Hashtable<String, String>();
boolean notifyLoaded = false;
String[] modelfilenames = getPdbFile();
for (int pe = 0; pe < getPdbCount(); pe++)
{
boolean matches = false;
+ addSequence(pe, getSequence()[pe]);
if (fileName == null)
{
if (false)
// see JAL-623 - need method of matching pasted data up
{
pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
- pdbfile, DataSourceType.PASTE);
- pdbfile, AppletFormatAdapter.PASTE,
- getIProgressIndicator());
++ pdbfile, DataSourceType.PASTE, getIProgressIndicator());
getPdbEntry(modelnum).setFile("INLINE" + pdb.getId());
matches = true;
foundEntry = true;
// needs
// to be tested. See mantis bug
// https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
- String protocol = AppletFormatAdapter.URL;
+ DataSourceType protocol = DataSourceType.URL;
try
{
if (fl.exists())
{
- protocol = AppletFormatAdapter.FILE;
+ protocol = DataSourceType.FILE;
}
} catch (Exception e)
{
}
// Explicitly map to the filename used by Jmol ;
pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
- fileName, protocol);
+ fileName, protocol, getIProgressIndicator());
// pdbentry[pe].getFile(), protocol);
}
String chid = new String(pdb.getId() + ":"
+ pdb.getChains().elementAt(i).id);
chainFile.put(chid, fileName);
- chainNames.addElement(chid);
+ chainNames.add(chid);
}
notifyLoaded = true;
}
setLoadingFromArchive(false);
}
+ @Override
+ public List<String> getChainNames()
+ {
+ return chainNames;
+ }
+
+ protected abstract IProgressIndicator getIProgressIndicator();
+
public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
{
notifyAtomPicked(iatom, strMeasure, null);
}
@Override
- public Dimension resizeInnerPanel(String data)
+ public int[] resizeInnerPanel(String data)
{
// Jalview doesn't honour resize panel requests
return null;
import jalview.structures.models.AAStructureBindingModel;
import jalview.util.MessageManager;
import jalview.util.Platform;
+import jalview.ws.dbsources.Pdb;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Graphics;
import java.awt.Rectangle;
import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.io.BufferedReader;
import javax.swing.JColorChooser;
import javax.swing.JInternalFrame;
import javax.swing.JMenu;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JSplitPane;
+import javax.swing.SwingUtilities;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
import javax.swing.event.MenuEvent;
public class AppJmol extends StructureViewerBase
{
+ // ms to wait for Jmol to load files
+ private static final int JMOL_LOAD_TIMEOUT = 20000;
+
+ private static final String SPACE = " ";
+
+ private static final String BACKSLASH = "\"";
+
AppJmolBinding jmb;
JPanel scriptWindow;
// / TODO: check if protocol is needed to be set, and if chains are
// autodiscovered.
jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
- pdbentrys, seqs, null, null);
+ pdbentrys, seqs, null);
jmb.setLoadingFromArchive(true);
addAlignmentPanel(ap);
IProgressIndicator progressBar = null;
+ @Override
+ protected IProgressIndicator getIProgressIndicator()
+ {
+ return progressBar;
+ }
/**
* add a single PDB structure to a new or existing Jmol view
*
{
progressBar = ap.alignFrame;
jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
- pdbentrys, seqs, null, null);
+ pdbentrys, seqs, null);
addAlignmentPanel(ap);
useAlignmentPanelForColourbyseq(ap);
if (pdbentrys.length > 1)
jmb.setColourBySequence(true);
setSize(400, 400); // probably should be a configurable/dynamic default here
initMenus();
- worker = null;
- {
- addingStructures = false;
- worker = new Thread(this);
- worker.start();
- }
+ addingStructures = false;
+ worker = new Thread(this);
+ worker.start();
+
this.addInternalFrameListener(new InternalFrameAdapter()
{
@Override
scriptWindow.setVisible(false);
}
- jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow,
- null);
+ jmb.allocateViewer(renderPanel, true, "", null, null, "",
+ scriptWindow, null);
// jmb.newJmolPopup("Jmol");
if (command == null)
{
jmb.setFinishedInit(true);
}
- void setChainMenuItems(Vector<String> chains)
- {
- chainMenu.removeAll();
- if (chains == null)
- {
- return;
- }
- JMenuItem menuItem = new JMenuItem(
- MessageManager.getString("label.all"));
- menuItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- allChainsSelected = true;
- for (int i = 0; i < chainMenu.getItemCount(); i++)
- {
- if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
- {
- ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
- }
- }
- centerViewer();
- allChainsSelected = false;
- }
- });
-
- chainMenu.add(menuItem);
-
- for (String chain : chains)
- {
- menuItem = new JCheckBoxMenuItem(chain, true);
- menuItem.addItemListener(new ItemListener()
- {
- @Override
- public void itemStateChanged(ItemEvent evt)
- {
- if (!allChainsSelected)
- {
- centerViewer();
- }
- }
- });
boolean allChainsSelected = false;
- void centerViewer()
+ @Override
+ void showSelectedChains()
{
Vector<String> toshow = new Vector<String>();
for (int i = 0; i < chainMenu.getItemCount(); i++)
public void run()
{
_started = true;
+ try
+ {
+ List<String> files = fetchPdbFiles();
+ if (files.size() > 0)
+ {
+ showFilesInViewer(files);
+ }
+ } finally
+ {
+ _started = false;
+ worker = null;
+ }
+ }
+
+ /**
+ * Either adds the given files to a structure viewer or opens a new viewer to
+ * show them
+ *
+ * @param files
+ * list of absolute paths to structure files
+ */
+ void showFilesInViewer(List<String> files)
+ {
+ long lastnotify = jmb.getLoadNotifiesHandled();
+ StringBuilder fileList = new StringBuilder();
+ for (String s : files)
+ {
+ fileList.append(SPACE).append(BACKSLASH)
+ .append(Platform.escapeString(s)).append(BACKSLASH);
+ }
+ String filesString = fileList.toString();
+
+ if (!addingStructures)
+ {
+ try
+ {
+ initJmol("load FILES " + filesString);
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("When trying to open the Jmol viewer!", oomerror);
+ Cache.log.debug("File locations are " + filesString);
+ } catch (Exception ex)
+ {
+ Cache.log.error("Couldn't open Jmol viewer!", ex);
+ }
+ }
+ else
+ {
+ StringBuilder cmd = new StringBuilder();
+ cmd.append("loadingJalviewdata=true\nload APPEND ");
+ cmd.append(filesString);
+ cmd.append("\nloadingJalviewdata=null");
+ final String command = cmd.toString();
+ lastnotify = jmb.getLoadNotifiesHandled();
+
+ try
+ {
+ jmb.evalStateCommand(command);
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("When trying to add structures to the Jmol viewer!",
+ oomerror);
+ Cache.log.debug("File locations are " + filesString);
+ } catch (Exception ex)
+ {
+ Cache.log.error("Couldn't add files to Jmol viewer!", ex);
+ }
+ }
+
+ // need to wait around until script has finished
+ int waitMax = JMOL_LOAD_TIMEOUT;
+ int waitFor = 35;
+ int waitTotal = 0;
+ while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
+ : !(jmb.isFinishedInit() && jmb.getPdbFile() != null && jmb
+ .getPdbFile().length == files.size()))
+ {
+ try
+ {
+ Cache.log.debug("Waiting around for jmb notify.");
+ Thread.sleep(waitFor);
+ waitTotal += waitFor;
+ } catch (Exception e)
+ {
+ }
+ if (waitTotal > waitMax)
+ {
+ System.err
+ .println("Timed out waiting for Jmol to load files after "
+ + waitTotal + "ms");
+// System.err.println("finished: " + jmb.isFinishedInit()
+// + "; loaded: " + Arrays.toString(jmb.getPdbFile())
+// + "; files: " + files.toString());
+ jmb.getPdbFile();
+ break;
+ }
+ }
+
+ // refresh the sequence colours for the new structure(s)
+ for (AlignmentPanel ap : _colourwith)
+ {
+ jmb.updateColours(ap);
+ }
+ // do superposition if asked to
+ if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures)
+ {
+ alignAddedStructures();
+ }
+ addingStructures = false;
+ }
+
+ /**
+ * Queues a thread to align structures with Jalview alignments
+ */
+ void alignAddedStructures()
+ {
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ if (jmb.viewer.isScriptExecuting())
+ {
+ SwingUtilities.invokeLater(this);
+ try
+ {
+ Thread.sleep(5);
+ } catch (InterruptedException q)
+ {
+ }
+ return;
+ }
+ else
+ {
+ alignStructs_withAllAlignPanels();
+ }
+ }
+ });
+ alignAddedStructures = false;
+ }
+
+ /**
+ * Retrieves and saves as file any modelled PDB entries for which we do not
+ * already have a file saved. Returns a list of absolute paths to structure
+ * files which were either retrieved, or already stored but not modelled in
+ * the structure viewer (i.e. files to add to the viewer display).
+ *
+ * @return
+ */
+ List<String> fetchPdbFiles()
+ {
+ // todo - record which pdbids were successfully imported.
+ StringBuilder errormsgs = new StringBuilder();
+
+ List<String> files = new ArrayList<String>();
String pdbid = "";
- // todo - record which pdbids were successfuly imported.
- StringBuffer errormsgs = new StringBuffer(), files = new StringBuffer();
try
{
- String[] curfiles = jmb.getPdbFile(); // files currently in viewer
+ String[] filesInViewer = jmb.getPdbFile();
// TODO: replace with reference fetching/transfer code (validate PDBentry
// as a DBRef?)
- jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb();
+ Pdb pdbclient = new Pdb();
for (int pi = 0; pi < jmb.getPdbCount(); pi++)
{
String file = jmb.getPdbEntry(pi).getFile();
} catch (Exception ex)
{
ex.printStackTrace();
- errormsgs.append("'" + pdbid + "'");
- }
- if (progressBar != null)
+ errormsgs.append("'").append(pdbid).append("'");
+ } finally
{
- progressBar.setProgressBar(
- MessageManager.getString("label.state_completed"), hdl);
+ if (progressBar != null)
+ {
+ progressBar.setProgressBar(
+ MessageManager.getString("label.state_completed"),
+ hdl);
+ }
}
if (pdbseq != null)
{
file = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
.elementAt(0).getFile()).getAbsolutePath();
jmb.getPdbEntry(pi).setFile(file);
-
- files.append(" \"" + Platform.escapeString(file) + "\"");
+ files.add(file);
}
else
{
- errormsgs.append("'" + pdbid + "' ");
+ errormsgs.append("'").append(pdbid).append("' ");
}
}
else
{
- if (curfiles != null && curfiles.length > 0)
+ if (filesInViewer != null && filesInViewer.length > 0)
{
addingStructures = true; // already files loaded.
- for (int c = 0; c < curfiles.length; c++)
+ for (int c = 0; c < filesInViewer.length; c++)
{
- if (curfiles[c].equals(file))
+ if (filesInViewer[c].equals(file))
{
file = null;
break;
}
if (file != null)
{
- files.append(" \"" + Platform.escapeString(file) + "\"");
+ files.add(file);
}
}
}
} catch (Exception ex)
{
ex.printStackTrace();
- errormsgs.append("When retrieving pdbfiles : current was: '" + pdbid
- + "'");
+ errormsgs.append("When retrieving pdbfiles : current was: '")
+ .append(pdbid).append("'");
}
if (errormsgs.length() > 0)
{
-
- JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
.formatMessage("label.pdb_entries_couldnt_be_retrieved",
new String[] { errormsgs.toString() }),
MessageManager.getString("label.couldnt_load_file"),
- JOptionPane.ERROR_MESSAGE);
-
- }
- long lastnotify = jmb.getLoadNotifiesHandled();
- if (files.length() > 0)
- {
- if (!addingStructures)
- {
-
- try
- {
- initJmol("load FILES " + files.toString());
- } catch (OutOfMemoryError oomerror)
- {
- new OOMWarning("When trying to open the Jmol viewer!", oomerror);
- Cache.log.debug("File locations are " + files);
- } catch (Exception ex)
- {
- Cache.log.error("Couldn't open Jmol viewer!", ex);
- }
- }
- else
- {
- StringBuffer cmd = new StringBuffer();
- cmd.append("loadingJalviewdata=true\nload APPEND ");
- cmd.append(files.toString());
- cmd.append("\nloadingJalviewdata=null");
- final String command = cmd.toString();
- cmd = null;
- lastnotify = jmb.getLoadNotifiesHandled();
-
- try
- {
- jmb.evalStateCommand(command);
- } catch (OutOfMemoryError oomerror)
- {
- new OOMWarning(
- "When trying to add structures to the Jmol viewer!",
- oomerror);
- Cache.log.debug("File locations are " + files);
- } catch (Exception ex)
- {
- Cache.log.error("Couldn't add files to Jmol viewer!", ex);
- }
- }
-
- // need to wait around until script has finished
- while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
- : (!jmb.isFinishedInit() && jmb.getPdbFile() != null && jmb
- .getPdbFile().length != jmb.getPdbCount()))
- {
- try
- {
- Cache.log.debug("Waiting around for jmb notify.");
- Thread.sleep(35);
- } catch (Exception e)
- {
- }
- }
-
- // refresh the sequence colours for the new structure(s)
- for (AlignmentPanel ap : _colourwith)
- {
- jmb.updateColours(ap);
- }
- // do superposition if asked to
- if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures)
- {
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- @Override
- public void run()
- {
- if (jmb.viewer.isScriptExecuting())
- {
- javax.swing.SwingUtilities.invokeLater(this);
- try
- {
- Thread.sleep(5);
- } catch (InterruptedException q)
- {
- }
- ;
- return;
- }
- else
- {
- alignStructs_withAllAlignPanels();
- }
- }
- });
- alignAddedStructures = false;
- }
- addingStructures = false;
-
+ JvOptionPane.ERROR_MESSAGE);
}
- _started = false;
- worker = null;
+ return files;
}
@Override
repaint();
return;
}
- setChainMenuItems(jmb.chainNames);
+ setChainMenuItems(jmb.getChainNames());
this.setTitle(jmb.getViewerTitle());
if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1)
package jalview.gui;
import jalview.api.AlignmentViewPanel;
+import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JalviewJmolBinding;
+import jalview.io.DataSourceType;
import jalview.structure.StructureSelectionManager;
import java.awt.Container;
private FeatureRenderer fr = null;
public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
- PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
- String protocol)
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs, DataSourceType protocol)
{
- super(sSm, pdbentry, sequenceIs, chains, protocol);
+ super(sSm, pdbentry, sequenceIs, protocol);
appJmolWindow = appJmol;
}
@Override
+ protected IProgressIndicator getIProgressIndicator()
+ {
+ return appJmolWindow.progressBar;
+ }
+ @Override
public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
{
AlignmentPanel ap = (alignment == null) ? appJmolWindow
// TODO Auto-generated method stub
return null;
}
+
+ @Override
+ public JalviewStructureDisplayI getViewer()
+ {
+ return appJmolWindow;
+ }
}
import jalview.datamodel.SequenceI;
import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
import jalview.gui.StructureViewer.ViewerType;
-import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
+import jalview.io.StructureFile;
import jalview.schemes.BuriedColourScheme;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.HelixColourScheme;
import jalview.ws.dbsources.Pdb;
import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.io.BufferedReader;
import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.List;
-import java.util.Map;
import java.util.Random;
-import java.util.Set;
import java.util.Vector;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JColorChooser;
import javax.swing.JInternalFrame;
import javax.swing.JMenu;
- import javax.swing.JOptionPane;
-import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
import javax.swing.event.MenuEvent;
public ChimeraViewFrame(PDBEntry pdbentry, SequenceI[] seq,
String[] chains, final AlignmentPanel ap)
{
- super();
+ this();
String pdbId = pdbentry.getId();
/*
SequenceI[][] seqs)
{
createProgressBar();
- String[][] chains = extractChains(seqs);
+ // FIXME extractChains needs pdbentries to match IDs to PDBEntry(s) on seqs
jmb = new JalviewChimeraBindingModel(this,
- ap.getStructureSelectionManager(), pdbentrys, seqs, chains,
- null);
+ ap.getStructureSelectionManager(), pdbentrys, seqs, null);
addAlignmentPanel(ap);
useAlignmentPanelForColourbyseq(ap);
if (pdbentrys.length > 1)
}
- /**
- * Retrieve chains for sequences by inspecting their PDB refs. The hope is
- * that the first will be to the sequence's own chain. Really need a more
- * managed way of doing this.
- *
- * @param seqs
- * @return
- */
- protected String[][] extractChains(SequenceI[][] seqs)
- {
- String[][] chains = new String[seqs.length][];
- for (int i = 0; i < seqs.length; i++)
- {
- chains[i] = new String[seqs[i].length];
- int seqno = 0;
- for (SequenceI seq : seqs[i])
- {
- String chain = null;
- if (seq.getDatasetSequence() != null)
- {
- Vector<PDBEntry> pdbrefs = seq.getDatasetSequence()
- .getAllPDBEntries();
- if (pdbrefs != null && pdbrefs.size() > 0)
- {
- chain = pdbrefs.get(0).getChainCode();
- }
- }
- chains[i][seqno++] = chain;
- }
- }
- return chains;
- }
+
/**
* Create a new viewer from saved session state data including Chimera session
SequenceI[][] seqsArray, boolean colourByChimera,
boolean colourBySequence, String newViewId)
{
- super();
+ this();
setViewId(newViewId);
this.chimeraSessionFile = chimeraSessionFile;
openNewChimera(alignPanel, pdbArray, seqsArray);
public ChimeraViewFrame(PDBEntry[] pe, SequenceI[][] seqs,
AlignmentPanel ap)
{
- super();
+ this();
openNewChimera(ap, pe, seqs);
}
- public ChimeraViewFrame(Map<PDBEntry, List<SequenceI>> toView,
- AlignmentPanel alignPanel)
+ /**
+ * Default constructor
+ */
+ public ChimeraViewFrame()
{
super();
/*
- * Convert the map of sequences per pdb entry into the tied arrays expected
- * by openNewChimera
- *
- * TODO pass the Map down to openNewChimera and its callees instead
+ * closeViewer will decide whether or not to close this frame
+ * depending on whether user chooses to Cancel or not
*/
- final Set<PDBEntry> pdbEntries = toView.keySet();
- PDBEntry[] pdbs = pdbEntries.toArray(new PDBEntry[pdbEntries.size()]);
- SequenceI[][] seqsForPdbs = new SequenceI[pdbEntries.size()][];
- for (int i = 0; i < pdbs.length; i++)
- {
- final List<SequenceI> seqsForPdb = toView.get(pdbs[i]);
- seqsForPdbs[i] = seqsForPdb.toArray(new SequenceI[seqsForPdb.size()]);
- }
-
- openNewChimera(alignPanel, pdbs, seqsForPdbs);
+ setDefaultCloseOperation(JInternalFrame.DO_NOTHING_ON_CLOSE);
}
/**
if (!jmb.launchChimera())
{
- JOptionPane.showMessageDialog(Desktop.desktop,
+ JvOptionPane.showMessageDialog(Desktop.desktop,
MessageManager.getString("label.chimera_failed"),
MessageManager.getString("label.error_loading_file"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
this.dispose();
return;
}
jmb.startChimeraListener();
}
- /**
- * If the list is not empty, add menu items for 'All' and each individual
- * chain to the "View | Show Chain" sub-menu. Multiple selections are allowed.
- *
- * @param chainNames
- */
- void setChainMenuItems(List<String> chainNames)
- {
- chainMenu.removeAll();
- if (chainNames == null || chainNames.isEmpty())
- {
- return;
- }
- JMenuItem menuItem = new JMenuItem(
- MessageManager.getString("label.all"));
- menuItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- allChainsSelected = true;
- for (int i = 0; i < chainMenu.getItemCount(); i++)
- {
- if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
- {
- ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
- }
- }
- showSelectedChains();
- allChainsSelected = false;
- }
- });
-
- chainMenu.add(menuItem);
-
- for (String chainName : chainNames)
- {
- menuItem = new JCheckBoxMenuItem(chainName, true);
- menuItem.addItemListener(new ItemListener()
- {
- @Override
- public void itemStateChanged(ItemEvent evt)
- {
- if (!allChainsSelected)
- {
- showSelectedChains();
- }
- }
- });
-
- chainMenu.add(menuItem);
- }
- }
/**
* Show only the selected chain(s) in the viewer
*/
+ @Override
void showSelectedChains()
{
List<String> toshow = new ArrayList<String>();
"label.confirm_close_chimera",
new Object[] { jmb.getViewerTitle("Chimera", false) });
prompt = JvSwingUtils.wrapTooltip(true, prompt);
- int confirm = JOptionPane.showConfirmDialog(this, prompt,
+ int confirm = JvOptionPane.showConfirmDialog(this, prompt,
MessageManager.getString("label.close_viewer"),
- JOptionPane.YES_NO_OPTION);
- closeChimera = confirm == JOptionPane.YES_OPTION;
+ JvOptionPane.YES_NO_CANCEL_OPTION);
+ /*
+ * abort closure if user hits escape or Cancel
+ */
+ if (confirm == JvOptionPane.CANCEL_OPTION
+ || confirm == JvOptionPane.CLOSED_OPTION)
+ {
+ return;
+ }
+ closeChimera = confirm == JvOptionPane.YES_OPTION;
}
jmb.closeViewer(closeChimera);
}
// TODO: check for memory leaks where instance isn't finalised because jmb
// holds a reference to the window
jmb = null;
+ dispose();
}
/**
List<PDBEntry> filePDB = new ArrayList<PDBEntry>();
List<Integer> filePDBpos = new ArrayList<Integer>();
PDBEntry thePdbEntry = null;
+ StructureFile pdb = null;
try
{
String[] curfiles = jmb.getPdbFile(); // files currently in viewer
if (errormsgs.length() > 0)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
.formatMessage("label.pdb_entries_couldnt_be_retrieved",
new Object[] { errormsgs.toString() }),
MessageManager.getString("label.couldnt_load_file"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
}
if (files.length() > 0)
{
int pos = filePDBpos.get(num).intValue();
long startTime = startProgressBar("Chimera "
- + MessageManager.getString("status.opening_file"));
+ + MessageManager.getString("status.opening_file_for")
+ + " " + pe.getId());
jmb.openFile(pe);
jmb.addSequence(pos, jmb.getSequence()[pos]);
File fl = new File(pe.getFile());
- String protocol = AppletFormatAdapter.URL;
+ DataSourceType protocol = DataSourceType.URL;
try
{
if (fl.exists())
{
- protocol = AppletFormatAdapter.FILE;
+ protocol = DataSourceType.FILE;
}
} catch (Throwable e)
{
stopProgressBar("", startTime);
}
// Explicitly map to the filename used by Chimera ;
- jmb.getSsm().setMapping(jmb.getSequence()[pos],
+ pdb = jmb.getSsm().setMapping(jmb.getSequence()[pos],
- jmb.getChains()[pos], pe.getFile(), protocol);
+ jmb.getChains()[pos], pe.getFile(), protocol,
+ progressBar);
+ stashFoundChains(pdb, pe.getFile());
} catch (OutOfMemoryError oomerror)
{
new OOMWarning(
}
}
}
+ jmb.refreshGUI();
jmb.setFinishedInit(true);
jmb.setLoadingFromArchive(false);
/**
* Fetch PDB data and save to a local file. Returns the full path to the file,
- * or null if fetch fails.
+ * or null if fetch fails. TODO: refactor to common with Jmol ? duplication
*
* @param processingEntry
* @return
* @throws Exception
*/
+
+ private void stashFoundChains(StructureFile pdb, String file)
+ {
+ for (int i = 0; i < pdb.getChains().size(); i++)
+ {
+ String chid = new String(pdb.getId() + ":"
+ + pdb.getChains().elementAt(i).id);
+ jmb.getChainNames().add(chid);
+ jmb.getChainFile().put(chid, file);
+ }
+ }
private String fetchPdbFile(PDBEntry processingEntry) throws Exception
{
+ // FIXME: this is duplicated code with Jmol frame ?
String filePath = null;
Pdb pdbclient = new Pdb();
AlignmentI pdbseq = null;
{
return jmb;
}
+
+ @Override
+ protected IProgressIndicator getIProgressIndicator()
+ {
+ return progressBar;
+ }
}
*/
package jalview.gui;
+import jalview.analysis.Conservation;
+import jalview.api.FeatureColourI;
import jalview.api.ViewStyleI;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.datamodel.StructureViewerModel.StructureData;
import jalview.ext.varna.RnaModel;
import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
import jalview.schemabinding.version2.AlcodMap;
import jalview.schemabinding.version2.AlcodonFrame;
import jalview.schemabinding.version2.Annotation;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.GraduatedColor;
+import jalview.schemes.FeatureColour;
import jalview.schemes.ResidueColourScheme;
import jalview.schemes.ResidueProperties;
import jalview.schemes.UserColourScheme;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Enumeration;
import java.util.HashMap;
import java.util.HashSet;
import java.util.jar.JarOutputStream;
import javax.swing.JInternalFrame;
--import javax.swing.JOptionPane;
import javax.swing.SwingUtilities;
import org.exolab.castor.xml.Marshaller;
*/
Map<String, SequenceI> seqRefIds = null;
- Vector<Object[]> frefedSequence = null;
+ Map<String, SequenceI> incompleteSeqs = null;
+
+ List<SeqFref> frefedSequence = null;
boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
{
seqsToIds.clear();
}
+ if (incompleteSeqs != null)
+ {
+ incompleteSeqs.clear();
+ }
// seqRefIds = null;
// seqsToIds = null;
}
{
seqRefIds = new HashMap<String, SequenceI>();
}
+ if (incompleteSeqs == null)
+ {
+ incompleteSeqs = new HashMap<String, SequenceI>();
+ }
+ if (frefedSequence == null)
+ {
+ frefedSequence = new ArrayList<SeqFref>();
+ }
}
public Jalview2XML()
this.raiseGUI = raiseGUI;
}
+ /**
+ * base class for resolving forward references to sequences by their ID
+ *
+ * @author jprocter
+ *
+ */
+ abstract class SeqFref
+ {
+ String sref;
+
+ String type;
+
+ public SeqFref(String _sref, String type)
+ {
+ sref = _sref;
+ this.type = type;
+ }
+
+ public String getSref()
+ {
+ return sref;
+ }
+
+ public SequenceI getSrefSeq()
+ {
+ return seqRefIds.get(sref);
+ }
+
+ public boolean isResolvable()
+ {
+ return seqRefIds.get(sref) != null;
+ }
+
+ public SequenceI getSrefDatasetSeq()
+ {
+ SequenceI sq = seqRefIds.get(sref);
+ if (sq != null)
+ {
+ while (sq.getDatasetSequence() != null)
+ {
+ sq = sq.getDatasetSequence();
+ }
+ }
+ return sq;
+ }
+
+ /**
+ * @return true if the forward reference was fully resolved
+ */
+ abstract boolean resolve();
+
+ @Override
+ public String toString()
+ {
+ return type + " reference to " + sref;
+ }
+ }
+
+ /**
+ * create forward reference for a mapping
+ *
+ * @param sref
+ * @param _jmap
+ * @return
+ */
+ public SeqFref newMappingRef(final String sref,
+ final jalview.datamodel.Mapping _jmap)
+ {
+ SeqFref fref = new SeqFref(sref, "Mapping")
+ {
+ public jalview.datamodel.Mapping jmap = _jmap;
+
+ @Override
+ boolean resolve()
+ {
+ SequenceI seq = getSrefDatasetSeq();
+ if (seq == null)
+ {
+ return false;
+ }
+ jmap.setTo(seq);
+ return true;
+ }
+ };
+ return fref;
+ }
+
+ public SeqFref newAlcodMapRef(final String sref,
+ final AlignedCodonFrame _cf, final jalview.datamodel.Mapping _jmap)
+ {
+
+ SeqFref fref = new SeqFref(sref, "Codon Frame")
+ {
+ AlignedCodonFrame cf = _cf;
+
+ public jalview.datamodel.Mapping mp = _jmap;
+
+ @Override
+ public boolean isResolvable()
+ {
+ return super.isResolvable() && mp.getTo() != null;
+ };
+
+ @Override
+ boolean resolve()
+ {
+ SequenceI seq = getSrefDatasetSeq();
+ if (seq == null)
+ {
+ return false;
+ }
+ cf.addMap(seq, mp.getTo(), mp.getMap());
+ return true;
+ }
+ };
+ return fref;
+ }
+
public void resolveFrefedSequences()
{
- if (frefedSequence.size() > 0)
+ Iterator<SeqFref> nextFref = frefedSequence.iterator();
+ int toresolve = frefedSequence.size();
+ int unresolved = 0, failedtoresolve = 0;
+ while (nextFref.hasNext())
{
- int r = 0, rSize = frefedSequence.size();
- while (r < rSize)
+ SeqFref ref = nextFref.next();
+ if (ref.isResolvable())
{
- Object[] ref = frefedSequence.elementAt(r);
- if (ref != null)
+ try
{
- String sref = (String) ref[0];
- if (seqRefIds.containsKey(sref))
+ if (ref.resolve())
{
- if (ref[1] instanceof jalview.datamodel.Mapping)
- {
- SequenceI seq = seqRefIds.get(sref);
- while (seq.getDatasetSequence() != null)
- {
- seq = seq.getDatasetSequence();
- }
- ((jalview.datamodel.Mapping) ref[1]).setTo(seq);
- }
- else
- {
- if (ref[1] instanceof jalview.datamodel.AlignedCodonFrame)
- {
- SequenceI seq = seqRefIds.get(sref);
- while (seq.getDatasetSequence() != null)
- {
- seq = seq.getDatasetSequence();
- }
- if (ref[2] != null
- && ref[2] instanceof jalview.datamodel.Mapping)
- {
- jalview.datamodel.Mapping mp = (jalview.datamodel.Mapping) ref[2];
- ((jalview.datamodel.AlignedCodonFrame) ref[1]).addMap(
- seq, mp.getTo(), mp.getMap());
- }
- else
- {
- System.err
- .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for AlcodonFrames involving "
- + ref[2].getClass() + " type objects.");
- }
- }
- else
- {
- System.err
- .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for "
- + ref[1].getClass() + " type objects.");
- }
- }
- frefedSequence.remove(r);
- rSize--;
+ nextFref.remove();
}
else
{
- System.err
- .println("IMPLEMENTATION WARNING: Unresolved forward reference for hash string "
- + ref[0]
- + " with objecttype "
- + ref[1].getClass());
- r++;
+ failedtoresolve++;
}
+ } catch (Exception x)
+ {
+ System.err
+ .println("IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence "
+ + ref.getSref());
+ x.printStackTrace();
+ failedtoresolve++;
}
- else
+ }
+ else
+ {
+ unresolved++;
+ }
+ }
+ if (unresolved > 0)
+ {
+ System.err.println("Jalview Project Import: There were " + unresolved
+ + " forward references left unresolved on the stack.");
+ }
+ if (failedtoresolve > 0)
+ {
+ System.err.println("SERIOUS! " + failedtoresolve
+ + " resolvable forward references failed to resolve.");
+ }
+ if (incompleteSeqs != null && incompleteSeqs.size() > 0)
+ {
+ System.err.println("Jalview Project Import: There are "
+ + incompleteSeqs.size()
+ + " sequences which may have incomplete metadata.");
+ if (incompleteSeqs.size() < 10)
+ {
+ for (SequenceI s : incompleteSeqs.values())
{
- // empty reference
- frefedSequence.remove(r);
- rSize--;
+ System.err.println(s.toString());
}
}
+ else
+ {
+ System.err
+ .println("Too many to report. Skipping output of incomplete sequences.");
+ }
}
}
{
return;
}
+ saveAllFrames(Arrays.asList(frames), jout);
+ }
+ /**
+ * core method for storing state for a set of AlignFrames.
+ *
+ * @param frames
+ * - frames involving all data to be exported (including containing
+ * splitframes)
+ * @param jout
+ * - project output stream
+ */
+ private void saveAllFrames(List<AlignFrame> frames, JarOutputStream jout)
+ {
Hashtable<String, AlignFrame> dsses = new Hashtable<String, AlignFrame>();
/*
List<String> viewIds = new ArrayList<String>();
// REVERSE ORDER
- for (int i = frames.length - 1; i > -1; i--)
+ for (int i = frames.size() - 1; i > -1; i--)
{
- AlignFrame af = frames[i];
+ AlignFrame af = frames.get(i);
// skip ?
if (skipList != null
&& skipList
{
try
{
- int ap = 0;
- int apSize = af.alignPanels.size();
FileOutputStream fos = new FileOutputStream(jarFile);
JarOutputStream jout = new JarOutputStream(fos);
- Hashtable<String, AlignFrame> dsses = new Hashtable<String, AlignFrame>();
- List<String> viewIds = new ArrayList<String>();
+ List<AlignFrame> frames = new ArrayList<AlignFrame>();
- for (AlignmentPanel apanel : af.alignPanels)
+ // resolve splitframes
+ if (af.getViewport().getCodingComplement() != null)
{
- String jfileName = apSize == 1 ? fileName : fileName + ap;
- ap++;
- if (!jfileName.endsWith(".xml"))
- {
- jfileName = jfileName + ".xml";
- }
- saveState(apanel, jfileName, jout, viewIds);
- String dssid = getDatasetIdRef(af.getViewport().getAlignment()
- .getDataset());
- if (!dsses.containsKey(dssid))
- {
- dsses.put(dssid, af);
- }
+ frames = ((SplitFrame) af.getSplitViewContainer()).getAlignFrames();
}
- writeDatasetFor(dsses, fileName, jout);
+ else
+ {
+ frames.add(af);
+ }
+ saveAllFrames(frames, jout);
try
{
jout.flush();
object.setVersion(jalview.bin.Cache.getDefault("VERSION",
"Development Build"));
- jalview.datamodel.AlignmentI jal = av.getAlignment();
+ /**
+ * rjal is full height alignment, jal is actual alignment with full metadata
+ * but excludes hidden sequences.
+ */
+ jalview.datamodel.AlignmentI rjal = av.getAlignment(), jal = rjal;
if (av.hasHiddenRows())
{
- jal = jal.getHiddenSequences().getFullAlignment();
+ rjal = jal.getHiddenSequences().getFullAlignment();
}
SequenceSet vamsasSet = new SequenceSet();
{
// switch jal and the dataset
jal = jal.getDataset();
+ rjal = jal;
}
}
if (jal.getProperties() != null)
JSeq jseq;
Set<String> calcIdSet = new HashSet<String>();
-
+ // record the set of vamsas sequence XML POJO we create.
+ HashMap<String, Sequence> vamsasSetIds = new HashMap<String, Sequence>();
// SAVE SEQUENCES
- for (int i = 0; i < jal.getHeight(); i++)
+ for (final SequenceI jds : rjal.getSequences())
{
final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds
: jds.getDatasetSequence();
String id = seqHash(jds);
-
- if (seqRefIds.get(id) != null)
- {
- // This happens for two reasons: 1. multiple views are being serialised.
- // 2. the hashCode has collided with another sequence's code. This DOES
- // HAPPEN! (PF00072.15.stk does this)
- // JBPNote: Uncomment to debug writing out of files that do not read
- // back in due to ArrayOutOfBoundExceptions.
- // System.err.println("vamsasSeq backref: "+id+"");
- // System.err.println(jds.getName()+"
- // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
- // System.err.println("Hashcode: "+seqHash(jds));
- // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
- // System.err.println(rsq.getName()+"
- // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
- // System.err.println("Hashcode: "+seqHash(rsq));
- }
- else
+ if (vamsasSetIds.get(id) == null)
{
- vamsasSeq = createVamsasSequence(id, jds);
- vamsasSet.addSequence(vamsasSeq);
- seqRefIds.put(id, jds);
+ if (seqRefIds.get(id) != null && !storeDS)
+ {
+ // This happens for two reasons: 1. multiple views are being
+ // serialised.
+ // 2. the hashCode has collided with another sequence's code. This
+ // DOES
+ // HAPPEN! (PF00072.15.stk does this)
+ // JBPNote: Uncomment to debug writing out of files that do not read
+ // back in due to ArrayOutOfBoundExceptions.
+ // System.err.println("vamsasSeq backref: "+id+"");
+ // System.err.println(jds.getName()+"
+ // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
+ // System.err.println("Hashcode: "+seqHash(jds));
+ // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
+ // System.err.println(rsq.getName()+"
+ // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
+ // System.err.println("Hashcode: "+seqHash(rsq));
+ }
+ else
+ {
+ vamsasSeq = createVamsasSequence(id, jds);
+ vamsasSet.addSequence(vamsasSeq);
+ vamsasSetIds.put(id, vamsasSeq);
+ seqRefIds.put(id, jds);
+ }
}
-
jseq = new JSeq();
jseq.setStart(jds.getStart());
jseq.setEnd(jds.getEnd());
// Store any sequences this sequence represents
if (av.hasHiddenRows())
{
+ // use rjal, contains the full height alignment
jseq.setHidden(av.getAlignment().getHiddenSequences()
.isHidden(jds));
- if (av.isHiddenRepSequence(jal.getSequenceAt(i)))
+ if (av.isHiddenRepSequence(jds))
{
jalview.datamodel.SequenceI[] reps = av
- .getRepresentedSequences(jal.getSequenceAt(i))
- .getSequencesInOrder(jal);
+ .getRepresentedSequences(jds).getSequencesInOrder(rjal);
for (int h = 0; h < reps.length; h++)
{
- if (reps[h] != jal.getSequenceAt(i))
+ if (reps[h] != jds)
{
- jseq.addHiddenSequences(jal.findIndex(reps[h]));
+ jseq.addHiddenSequences(rjal.findIndex(reps[h]));
}
}
}
}
+ // mark sequence as reference - if it is the reference for this view
+ if (jal.hasSeqrep())
+ {
+ jseq.setViewreference(jds == jal.getSeqrep());
+ }
}
+ // TODO: omit sequence features from each alignment view's XML dump if we
+ // are storing dataset
if (jds.getSequenceFeatures() != null)
{
jalview.datamodel.SequenceFeature[] sf = jds.getSequenceFeatures();
}
}
- if (entry.getProperty() != null && !entry.getProperty().isEmpty())
+ Enumeration<String> props = entry.getProperties();
+ if (props.hasMoreElements())
{
PdbentryItem item = new PdbentryItem();
- Hashtable properties = entry.getProperty();
- Enumeration en2 = properties.keys();
- while (en2.hasMoreElements())
+ while (props.hasMoreElements())
{
Property prop = new Property();
- String key = en2.nextElement().toString();
+ String key = props.nextElement();
prop.setName(key);
- prop.setValue(properties.get(key).toString());
+ prop.setValue(entry.getProperty(key).toString());
item.addProperty(prop);
}
pdb.addPdbentryItem(item);
jal = av.getAlignment();
}
// SAVE MAPPINGS
- if (jal.getCodonFrames() != null)
+ // FOR DATASET
+ if (storeDS && jal.getCodonFrames() != null)
{
List<AlignedCodonFrame> jac = jal.getCodonFrames();
for (AlignedCodonFrame acf : jac)
{
AlcodonFrame alc = new AlcodonFrame();
if (acf.getProtMappings() != null
&& acf.getProtMappings().length > 0)
{
+ boolean hasMap = false;
SequenceI[] dnas = acf.getdnaSeqs();
jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
for (int m = 0; m < pmaps.length; m++)
alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
false));
alc.addAlcodMap(alcmap);
+ hasMap = true;
+ }
+ if (hasMap)
+ {
+ vamsasSet.addAlcodonFrame(alc);
}
}
-
+ // TODO: delete this ? dead code from 2.8.3->2.9 ?
// {
// AlcodonFrame alc = new AlcodonFrame();
// vamsasSet.addAlcodonFrame(alc);
.toArray(new String[0]);
Vector<String> settingsAdded = new Vector<String>();
- Object gstyle = null;
- GraduatedColor gcol = null;
if (renderOrder != null)
{
for (String featureType : renderOrder)
{
- gstyle = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
- .getFeatureStyle(featureType);
+ FeatureColourI fcol = ap.getSeqPanel().seqCanvas
+ .getFeatureRenderer().getFeatureStyle(featureType);
Setting setting = new Setting();
setting.setType(featureType);
- if (gstyle instanceof GraduatedColor)
+ if (!fcol.isSimpleColour())
{
- 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());
+ setting.setColour(fcol.getMaxColour().getRGB());
+ setting.setMincolour(fcol.getMinColour().getRGB());
+ setting.setMin(fcol.getMin());
+ setting.setMax(fcol.getMax());
+ setting.setColourByLabel(fcol.isColourByLabel());
+ setting.setAutoScale(fcol.isAutoScaled());
+ setting.setThreshold(fcol.getThreshold());
+ // -1 = No threshold, 0 = Below, 1 = Above
+ setting.setThreshstate(fcol.isAboveThreshold() ? 1 : (fcol
+ .isBelowThreshold() ? 0 : -1));
}
else
{
- setting.setColour(((Color) gstyle).getRGB());
+ setting.setColour(fcol.getColour().getRGB());
}
setting.setDisplay(av.getFeaturesDisplayed().isVisible(
// is groups actually supposed to be a map here ?
Iterator<String> en = ap.getSeqPanel().seqCanvas
- .getFeatureRenderer()
- .getFeatureGroups().iterator();
+ .getFeatureRenderer().getFeatureGroups().iterator();
Vector<String> groupsAdded = new Vector<String>();
while (en.hasNext())
{
groupsAdded.addElement(grp);
}
jms.setFeatureSettings(fs);
-
}
if (av.hasHiddenColumns())
if (jds.getDatasetSequence() != null)
{
vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
}
else
{
- vamsasSeq.setDsseqid(id); // so we can tell which sequences really are
+ // seqId==dsseqid so we can tell which sequences really are
// dataset sequences only
+ vamsasSeq.setDsseqid(id);
dbrefs = jds.getDBRefs();
+ if (parentseq == null)
+ {
+ parentseq = jds;
+ }
}
if (dbrefs != null)
{
if (jmp.getTo() != null)
{
MappingChoice mpc = new MappingChoice();
- if (recurse
- && (parentseq != jmp.getTo() || parentseq
- .getDatasetSequence() != jmp.getTo()))
+
+ // check/create ID for the sequence referenced by getTo()
+
+ String jmpid = "";
+ SequenceI ps = null;
+ if (parentseq != jmp.getTo()
+ && parentseq.getDatasetSequence() != jmp.getTo())
{
- mpc.setSequence(createVamsasSequence(false, seqHash(jmp.getTo()),
- jmp.getTo(), jds));
+ // chaining dbref rather than a handshaking one
+ jmpid = seqHash(ps = jmp.getTo());
}
else
{
- String jmpid = "";
- SequenceI ps = null;
- if (parentseq != jmp.getTo()
- && parentseq.getDatasetSequence() != jmp.getTo())
- {
- // chaining dbref rather than a handshaking one
- jmpid = seqHash(ps = jmp.getTo());
- }
- else
- {
- jmpid = seqHash(ps = parentseq);
- }
- mpc.setDseqFor(jmpid);
- if (!seqRefIds.containsKey(mpc.getDseqFor()))
- {
- jalview.bin.Cache.log.debug("creatign new DseqFor ID");
- seqRefIds.put(mpc.getDseqFor(), ps);
- }
- else
- {
- jalview.bin.Cache.log.debug("reusing DseqFor ID");
- }
+ jmpid = seqHash(ps = parentseq);
+ }
+ mpc.setDseqFor(jmpid);
+ if (!seqRefIds.containsKey(mpc.getDseqFor()))
+ {
+ jalview.bin.Cache.log.debug("creatign new DseqFor ID");
+ seqRefIds.put(mpc.getDseqFor(), ps);
}
+ else
+ {
+ jalview.bin.Cache.log.debug("reusing DseqFor ID");
+ }
+
mp.setMappingChoice(mpc);
}
}
}
if (seqRefIds == null)
{
- seqRefIds = new HashMap<String, SequenceI>();
- }
- if (frefedSequence == null)
- {
- frefedSequence = new Vector<Object[]>();
+ initSeqRefs();
}
-
AlignFrame af = null, _af = null;
+ IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<AlignmentI, AlignmentI>();
Map<String, AlignFrame> gatherToThisFrame = new HashMap<String, AlignFrame>();
final String file = jprovider.getFilename();
try
if (true) // !skipViewport(object))
{
_af = loadFromObject(object, file, true, jprovider);
- if (object.getJalviewModelSequence().getViewportCount() > 0)
+ if (_af != null
+ && object.getJalviewModelSequence().getViewportCount() > 0)
{
- af = _af;
- if (af.viewport.isGatherViewsHere())
+ if (af == null)
+ {
+ // store a reference to the first view
+ af = _af;
+ }
+ if (_af.viewport.isGatherViewsHere())
{
- gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
+ // if this is a gathered view, keep its reference since
+ // after gathering views, only this frame will remain
+ af = _af;
+ gatherToThisFrame.put(_af.viewport.getSequenceSetId(), _af);
}
+ // Save dataset to register mappings once all resolved
+ importedDatasets.put(af.viewport.getAlignment().getDataset(),
+ af.viewport.getAlignment().getDataset());
}
}
entryCount++;
e.printStackTrace();
}
- if (Desktop.instance != null)
- {
- Desktop.instance.stopLoading();
- }
-
/*
* Regather multiple views (with the same sequence set id) to the frame (if
* any) that is flagged as the one to gather to, i.e. convert them to tabbed
}
restoreSplitFrames();
-
+ for (AlignmentI ds : importedDatasets.keySet())
+ {
+ if (ds.getCodonFrames() != null)
+ {
+ StructureSelectionManager.getStructureSelectionManager(
+ Desktop.instance).registerMappings(ds.getCodonFrames());
+ }
+ }
if (errorMessage != null)
{
reportErrors();
}
+
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.stopLoading();
+ }
+
return af;
}
SplitFrame sf = createSplitFrame(dnaFrame, af);
addedToSplitFrames.add(dnaFrame);
addedToSplitFrames.add(af);
+ dnaFrame.setMenusForViewport();
+ af.setMenusForViewport();
if (af.viewport.isGatherViewsHere())
{
gatherTo.add(sf);
Viewport view = candidate.getKey();
Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
view.getHeight());
+ af.setMenusForViewport();
System.err.println("Failed to restore view " + view.getTitle()
+ " to split frame");
}
@Override
public void run()
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
finalErrorMessage, "Error "
+ (saving ? "saving" : "loading")
- + " Jalview file", JOptionPane.WARNING_MESSAGE);
+ + " Jalview file", JvOptionPane.WARNING_MESSAGE);
}
});
}
* @param pdbId
* @return
*/
- String loadPDBFile(jarInputStreamProvider jprovider, String pdbId)
+ String loadPDBFile(jarInputStreamProvider jprovider, String pdbId,
+ String origFile)
{
if (alreadyLoadedPDB.containsKey(pdbId))
{
return alreadyLoadedPDB.get(pdbId).toString();
}
- String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb");
+ String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb",
+ origFile);
if (tempFile != null)
{
alreadyLoadedPDB.put(pdbId, tempFile);
* @param prefix
* a prefix for the temporary file name, must be at least three
* characters long
+ * @param origFile
+ * null or original file - so new file can be given the same suffix
+ * as the old one
* @return
*/
protected String copyJarEntry(jarInputStreamProvider jprovider,
- String jarEntryName, String prefix)
+ String jarEntryName, String prefix, String origFile)
{
BufferedReader in = null;
PrintWriter out = null;
-
+ String suffix = ".tmp";
+ if (origFile == null)
+ {
+ origFile = jarEntryName;
+ }
+ int sfpos = origFile.lastIndexOf(".");
+ if (sfpos > -1 && sfpos < (origFile.length() - 3))
+ {
+ suffix = "." + origFile.substring(sfpos + 1);
+ }
try
{
JarInputStream jin = jprovider.getJarInputStream();
if (entry != null)
{
in = new BufferedReader(new InputStreamReader(jin, UTF_8));
- File outFile = File.createTempFile(prefix, ".tmp");
+ File outFile = File.createTempFile(prefix, suffix);
outFile.deleteOnExit();
out = new PrintWriter(new FileOutputStream(outFile));
String data;
// LOAD SEQUENCES
List<SequenceI> hiddenSeqs = null;
- jalview.datamodel.Sequence jseq;
List<SequenceI> tmpseqs = new ArrayList<SequenceI>();
boolean multipleView = false;
-
+ SequenceI referenceseqForView = null;
JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
int vi = 0; // counter in vamsasSeq array
for (int i = 0; i < jseqs.length; i++)
{
String seqId = jseqs[i].getId();
- if (seqRefIds.get(seqId) != null)
+ SequenceI tmpSeq = seqRefIds.get(seqId);
+ if (tmpSeq != null)
{
- tmpseqs.add(seqRefIds.get(seqId));
- multipleView = true;
+ if (!incompleteSeqs.containsKey(seqId))
+ {
+ // may not need this check, but keep it for at least 2.9,1 release
+ if (tmpSeq.getStart() != jseqs[i].getStart()
+ || tmpSeq.getEnd() != jseqs[i].getEnd())
+ {
+ System.err
+ .println("Warning JAL-2154 regression: updating start/end for sequence "
+ + tmpSeq.toString() + " to " + jseqs[i]);
+ }
+ }
+ else
+ {
+ incompleteSeqs.remove(seqId);
+ }
+ if (vamsasSeq.length > vi && vamsasSeq[vi].getId().equals(seqId))
+ {
+ // most likely we are reading a dataset XML document so
+ // update from vamsasSeq section of XML for this sequence
+ tmpSeq.setName(vamsasSeq[vi].getName());
+ tmpSeq.setDescription(vamsasSeq[vi].getDescription());
+ tmpSeq.setSequence(vamsasSeq[vi].getSequence());
+ vi++;
+ }
+ else
+ {
+ // reading multiple views, so vamsasSeq set is a subset of JSeq
+ multipleView = true;
+ }
+ tmpSeq.setStart(jseqs[i].getStart());
+ tmpSeq.setEnd(jseqs[i].getEnd());
+ tmpseqs.add(tmpSeq);
}
else
{
- jseq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
+ tmpSeq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
vamsasSeq[vi].getSequence());
- jseq.setDescription(vamsasSeq[vi].getDescription());
- jseq.setStart(jseqs[i].getStart());
- jseq.setEnd(jseqs[i].getEnd());
- jseq.setVamsasId(uniqueSetSuffix + seqId);
- seqRefIds.put(vamsasSeq[vi].getId(), jseq);
- tmpseqs.add(jseq);
+ tmpSeq.setDescription(vamsasSeq[vi].getDescription());
+ tmpSeq.setStart(jseqs[i].getStart());
+ tmpSeq.setEnd(jseqs[i].getEnd());
+ tmpSeq.setVamsasId(uniqueSetSuffix + seqId);
+ seqRefIds.put(vamsasSeq[vi].getId(), tmpSeq);
+ tmpseqs.add(tmpSeq);
vi++;
}
+ if (jseqs[i].hasViewreference() && jseqs[i].getViewreference())
+ {
+ referenceseqForView = tmpseqs.get(tmpseqs.size() - 1);
+ }
+
if (jseqs[i].getHidden())
{
if (hiddenSeqs == null)
hiddenSeqs = new ArrayList<SequenceI>();
}
- hiddenSeqs.add(seqRefIds.get(seqId));
+ hiddenSeqs.add(tmpSeq);
}
-
}
// /
SequenceI[] orderedSeqs = tmpseqs
.toArray(new SequenceI[tmpseqs.size()]);
- Alignment al = new Alignment(orderedSeqs);
-
- // / Add the alignment properties
- for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
- {
- SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
- al.setProperty(ssp.getKey(), ssp.getValue());
- }
-
- // /
- // SequenceFeatures are added to the DatasetSequence,
- // so we must create or recover the dataset before loading features
+ AlignmentI al = null;
+ // so we must create or recover the dataset alignment before going further
// ///////////////////////////////
if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
{
- // older jalview projects do not have a dataset id.
+ // older jalview projects do not have a dataset - so creat alignment and
+ // dataset
+ al = new Alignment(orderedSeqs);
al.setDataset(null);
}
else
{
- // recover dataset - passing on flag indicating if this a 'viewless'
- // sequence set (a.k.a. a stored dataset for the project)
- recoverDatasetFor(vamsasSet, al, object.getJalviewModelSequence()
- .getViewportCount() == 0);
+ boolean isdsal = object.getJalviewModelSequence().getViewportCount() == 0;
+ if (isdsal)
+ {
+ // we are importing a dataset record, so
+ // recover reference to an alignment already materialsed as dataset
+ al = getDatasetFor(vamsasSet.getDatasetId());
+ }
+ if (al == null)
+ {
+ // materialse the alignment
+ al = new Alignment(orderedSeqs);
+ }
+ if (isdsal)
+ {
+ addDatasetRef(vamsasSet.getDatasetId(), al);
+ }
+
+ // finally, verify all data in vamsasSet is actually present in al
+ // passing on flag indicating if it is actually a stored dataset
+ recoverDatasetFor(vamsasSet, al, isdsal);
}
+
+ if (referenceseqForView != null)
+ {
+ al.setSeqrep(referenceseqForView);
+ }
+ // / Add the alignment properties
+ for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
+ {
+ SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
+ al.setProperty(ssp.getKey(), ssp.getValue());
+ }
+
// ///////////////////////////////
Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
{
// load sequence features, database references and any associated PDB
// structures for the alignment
+ //
+ // prior to 2.10, this part would only be executed the first time a
+ // sequence was encountered, but not afterwards.
+ // now, for 2.10 projects, this is also done if the xml doc includes
+ // dataset sequences not actually present in any particular view.
+ //
for (int i = 0; i < vamsasSeq.length; i++)
{
if (jseqs[i].getFeaturesCount() > 0)
}
}
-
- al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
+ // adds feature to datasequence's feature set (since Jalview 2.10)
+ al.getSequenceAt(i).addSequenceFeature(sf);
}
}
if (vamsasSeq[i].getDBRefCount() > 0)
{
- addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]);
+ // adds dbrefs to datasequence's set (since Jalview 2.10)
+ addDBRefs(
+ al.getSequenceAt(i).getDatasetSequence() == null ? al.getSequenceAt(i)
+ : al.getSequenceAt(i).getDatasetSequence(),
+ vamsasSeq[i]);
}
if (jseqs[i].getPdbidsCount() > 0)
{
entry.setId(ids[p].getId());
if (ids[p].getType() != null)
{
- if (ids[p].getType().equalsIgnoreCase("PDB"))
+ if (PDBEntry.Type.getType(ids[p].getType()) != null)
{
- entry.setType(PDBEntry.Type.PDB);
+ entry.setType(PDBEntry.Type.getType(ids[p].getType()));
}
else
{
entry.setType(PDBEntry.Type.FILE);
}
}
- if (ids[p].getFile() != null)
+ // jprovider is null when executing 'New View'
+ if (ids[p].getFile() != null && jprovider != null)
{
if (!pdbloaded.containsKey(ids[p].getFile()))
{
- entry.setFile(loadPDBFile(jprovider, ids[p].getId()));
+ entry.setFile(loadPDBFile(jprovider, ids[p].getId(),
+ ids[p].getFile()));
}
else
{
entry.setFile(pdbloaded.get(ids[p].getId()).toString());
}
}
+ if (ids[p].getPdbentryItem() != null)
+ {
+ for (PdbentryItem item : ids[p].getPdbentryItem())
+ {
+ for (Property pr : item.getProperty())
+ {
+ entry.setProperty(pr.getName(), pr.getValue());
+ }
+ }
+ }
StructureSelectionManager.getStructureSelectionManager(
Desktop.instance).registerPDBEntry(entry);
- al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
+ // adds PDBEntry to datasequence's set (since Jalview 2.10)
+ if (al.getSequenceAt(i).getDatasetSequence() != null)
+ {
+ al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
+ }
+ else
+ {
+ al.getSequenceAt(i).addPDBId(entry);
+ }
}
}
}
if (maps[m].getMapping() != null)
{
mapping = addMapping(maps[m].getMapping());
- }
- if (dnaseq != null && mapping.getTo() != null)
- {
- cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
- }
- else
- {
- // defer to later
- frefedSequence.add(new Object[] { maps[m].getDnasq(), cf,
- mapping });
+ if (dnaseq != null && mapping.getTo() != null)
+ {
+ cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
+ }
+ else
+ {
+ // defer to later
+ frefedSequence.add(newAlcodMapRef(maps[m].getDnasq(), cf,
+ mapping));
+ }
}
}
+ al.addCodonFrame(cf);
}
- al.addCodonFrame(cf);
}
}
}
if (jGroup.getConsThreshold() != 0)
{
- jalview.analysis.Conservation c = new jalview.analysis.Conservation(
- "All", ResidueProperties.propHash, 3,
- sg.getSequences(null), 0, sg.getWidth() - 1);
+ Conservation c = new Conservation("All", sg.getSequences(null),
+ 0, sg.getWidth() - 1);
c.calculate();
c.verdict(false, 25);
sg.cs.setConservation(c);
String rnaTitle = ss.getTitle();
String sessionState = ss.getViewerState();
String tempStateFile = copyJarEntry(jprovider, sessionState,
- "varna");
+ "varna", null);
RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
appVarna.addModelSession(rna, rnaTitle, tempStateFile);
}
// Originally : ids[p].getFile()
// : TODO: verify external PDB file recovery still works in normal
// jalview project load
- jpdb.setFile(loadPDBFile(jprovider, ids[p].getId()));
+ jpdb.setFile(loadPDBFile(jprovider, ids[p].getId(),
+ ids[p].getFile()));
jpdb.setId(ids[p].getId());
int x = structureState.getXpos();
// 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());
+ String pdbFile = loadPDBFile(jprovider, ids[p].getId(),
+ ids[p].getFile());
jalview.datamodel.SequenceI seq = seqRefIds.get(jseqs[i]
.getId() + "");
if (sviewid == null)
*/
String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
- "chimera");
+ "chimera", null);
Set<Entry<File, StructureData>> fileData = data.getFileData()
.entrySet();
// filename
// translation differently.
StructureData filedat = oldFiles.get(new File(oldfilenam));
+ if (filedat == null)
+ {
+ String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
+ filedat = oldFiles.get(new File(reformatedOldFilename));
+ }
newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
pdbfilenames.add(filedat.getFilePath());
pdbids.add(filedat.getPdbId());
StructureData filedat = oldFiles.get(id);
String pdbFile = filedat.getFilePath();
SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
- binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE);
- binding.getSsm().setMapping(seq, null, pdbFile,
- jalview.io.AppletFormatAdapter.FILE, null);
++ binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE,
++ null);
binding.addSequenceForStructFile(pdbFile, seq);
}
// and add the AlignmentPanel's reference to the view panel
}
AlignFrame loadViewport(String file, JSeq[] JSEQ,
- List<SequenceI> hiddenSeqs, Alignment al,
+ List<SequenceI> hiddenSeqs, AlignmentI al,
JalviewModelSequence jms, Viewport view, String uniqueSeqSetId,
String viewId, List<JvAnnotRow> autoAlan)
{
af = new AlignFrame(al, view.getWidth(), view.getHeight(),
uniqueSeqSetId, viewId);
- af.setFileName(file, "Jalview");
+ af.setFileName(file, FileFormat.Jalview);
for (int i = 0; i < JSEQ.length; i++)
{
.getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
}
+ if (al.hasSeqrep())
+ {
+ af.getViewport().setColourByReferenceSeq(true);
+ af.getViewport().setDisplayReferenceSeq(true);
+ }
+
af.viewport.setGatherViewsHere(view.getGatheredViews());
if (view.getSequenceSetId() != null)
{
for (int s = 0; s < JSEQ.length; s++)
{
- jalview.datamodel.SequenceGroup hidden = new jalview.datamodel.SequenceGroup();
-
+ SequenceGroup hidden = new SequenceGroup();
+ boolean isRepresentative = false;
for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
{
- hidden.addSequence(
- al.getSequenceAt(JSEQ[s].getHiddenSequences(r)), false);
+ isRepresentative = true;
+ SequenceI sequenceToHide = al.getSequenceAt(JSEQ[s]
+ .getHiddenSequences(r));
+ hidden.addSequence(sequenceToHide, false);
+ // remove from hiddenSeqs list so we don't try to hide it twice
+ hiddenSeqs.remove(sequenceToHide);
+ }
+ if (isRepresentative)
+ {
+ SequenceI representativeSequence = al.getSequenceAt(s);
+ hidden.addSequence(representativeSequence, false);
+ af.viewport.hideRepSequences(representativeSequence, hidden);
}
- af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
}
- // jalview.datamodel.SequenceI[] hseqs = new
- // jalview.datamodel.SequenceI[hiddenSeqs
- // .size()];
- //
- // for (int s = 0; s < hiddenSeqs.size(); s++)
- // {
- // hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s);
- // }
-
SequenceI[] hseqs = hiddenSeqs.toArray(new SequenceI[hiddenSeqs
.size()]);
af.viewport.hideSequence(hseqs);
af.viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
String[] renderOrder = new String[jms.getFeatureSettings()
.getSettingCount()];
- Hashtable featureGroups = new Hashtable();
- Hashtable featureColours = new Hashtable();
- Hashtable featureOrder = new Hashtable();
+ Map<String, FeatureColourI> featureColours = new Hashtable<String, FeatureColourI>();
+ Map<String, Float> featureOrder = new Hashtable<String, Float>();
for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
{
Setting setting = jms.getFeatureSettings().getSetting(fs);
if (setting.hasMincolour())
{
- GraduatedColor gc = setting.hasMin() ? new GraduatedColor(
- new java.awt.Color(setting.getMincolour()),
- new java.awt.Color(setting.getColour()),
- setting.getMin(), setting.getMax()) : new GraduatedColor(
- new java.awt.Color(setting.getMincolour()),
- new java.awt.Color(setting.getColour()), 0, 1);
+ FeatureColourI gc = setting.hasMin() ? new FeatureColour(
+ new Color(setting.getMincolour()), new Color(
+ setting.getColour()), setting.getMin(),
+ setting.getMax()) : new FeatureColour(new Color(
+ setting.getMincolour()), new Color(setting.getColour()),
+ 0, 1);
if (setting.hasThreshold())
{
- gc.setThresh(setting.getThreshold());
- gc.setThreshType(setting.getThreshstate());
+ gc.setThreshold(setting.getThreshold());
+ int threshstate = setting.getThreshstate();
+ // -1 = None, 0 = Below, 1 = Above threshold
+ if (threshstate == 0)
+ {
+ gc.setBelowThreshold(true);
+ }
+ else if (threshstate == 1)
+ {
+ gc.setAboveThreshold(true);
+ }
}
gc.setAutoScaled(true); // default
if (setting.hasAutoScale())
}
else
{
- featureColours.put(setting.getType(),
- new java.awt.Color(setting.getColour()));
+ featureColours.put(setting.getType(), new FeatureColour(
+ new Color(setting.getColour())));
}
renderOrder[fs] = setting.getType();
if (setting.hasOrder())
fdi.setVisible(setting.getType());
}
}
- Hashtable fgtable = new Hashtable();
+ Map<String, Boolean> fgtable = new Hashtable<String, Boolean>();
for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
{
Group grp = jms.getFeatureSettings().getGroup(gs);
}
}
af.setMenusFromViewport(af.viewport);
-
+ af.setTitle(view.getTitle());
// TODO: we don't need to do this if the viewport is aready visible.
/*
* Add the AlignFrame to the desktop (it may be 'gathered' later), unless it
}
private ColourSchemeI constructAnnotationColour(
- AnnotationColours viewAnnColour, AlignFrame af, Alignment al,
+ AnnotationColours viewAnnColour, AlignFrame af, AlignmentI al,
JalviewModelSequence jms, boolean checkGroupAnnColour)
{
boolean propagateAnnColour = false;
return cs;
}
- private void reorderAutoannotation(AlignFrame af, Alignment al,
+ private void reorderAutoannotation(AlignFrame af, AlignmentI al,
List<JvAnnotRow> autoAlan)
{
// copy over visualization settings for autocalculated annotation in the
}
}
- private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al,
+ private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al,
boolean ignoreUnrefed)
{
- jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId());
+ jalview.datamodel.AlignmentI ds = getDatasetFor(vamsasSet
+ .getDatasetId());
Vector dseqs = null;
if (ds == null)
{
for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
{
Sequence vamsasSeq = vamsasSet.getSequence(i);
- ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed);
+ ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed, i);
}
// create a new dataset
if (ds == null)
* dataset alignment
* @param dseqs
* vector to add new dataset sequence to
+ * @param ignoreUnrefed
+ * - when true, don't create new sequences from vamsasSeq if it's id
+ * doesn't already have an asssociated Jalview sequence.
+ * @param vseqpos
+ * - used to reorder the sequence in the alignment according to the
+ * vamsasSeq array ordering, to preserve ordering of dataset
*/
private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
- AlignmentI ds, Vector dseqs, boolean ignoreUnrefed)
+ AlignmentI ds, Vector dseqs, boolean ignoreUnrefed, int vseqpos)
{
// JBP TODO: Check this is called for AlCodonFrames to support recovery of
// xRef Codon Maps
SequenceI sq = seqRefIds.get(vamsasSeq.getId());
+ boolean reorder = false;
SequenceI dsq = null;
if (sq != null && sq.getDatasetSequence() != null)
{
dsq = sq.getDatasetSequence();
}
+ else
+ {
+ reorder = true;
+ }
if (sq == null && ignoreUnrefed)
{
return;
// + (post ? "appended" : ""));
}
}
+ else
+ {
+ // sequence refs are identical. We may need to update the existing dataset
+ // alignment with this one, though.
+ if (ds != null && dseqs == null)
+ {
+ int opos = ds.findIndex(dsq);
+ SequenceI tseq = null;
+ if (opos != -1 && vseqpos != opos)
+ {
+ // remove from old position
+ ds.deleteSequence(dsq);
+ }
+ if (vseqpos < ds.getHeight())
+ {
+ if (vseqpos != opos)
+ {
+ // save sequence at destination position
+ tseq = ds.getSequenceAt(vseqpos);
+ ds.replaceSequenceAt(vseqpos, dsq);
+ ds.addSequence(tseq);
+ }
+ }
+ else
+ {
+ ds.addSequence(dsq);
+ }
+ }
+ }
}
/*
* TODO use AlignmentI here and in related methods - needs
* AlignmentI.getDataset() changed to return AlignmentI instead of Alignment
*/
- Hashtable<String, Alignment> datasetIds = null;
+ Hashtable<String, AlignmentI> datasetIds = null;
- IdentityHashMap<Alignment, String> dataset2Ids = null;
+ IdentityHashMap<AlignmentI, String> dataset2Ids = null;
- private Alignment getDatasetFor(String datasetId)
+ private AlignmentI getDatasetFor(String datasetId)
{
if (datasetIds == null)
{
- datasetIds = new Hashtable<String, Alignment>();
+ datasetIds = new Hashtable<String, AlignmentI>();
return null;
}
if (datasetIds.containsKey(datasetId))
return null;
}
- private void addDatasetRef(String datasetId, Alignment dataset)
+ private void addDatasetRef(String datasetId, AlignmentI dataset)
{
if (datasetIds == null)
{
- datasetIds = new Hashtable<String, Alignment>();
+ datasetIds = new Hashtable<String, AlignmentI>();
}
datasetIds.put(datasetId, dataset);
}
* @param dataset
* @return
*/
- private String getDatasetIdRef(Alignment dataset)
+ private String getDatasetIdRef(AlignmentI dataset)
{
if (dataset.getDataset() != null)
{
// make a new datasetId and record it
if (dataset2Ids == null)
{
- dataset2Ids = new IdentityHashMap<Alignment, String>();
+ dataset2Ids = new IdentityHashMap<AlignmentI, String>();
}
else
{
}
else
{
- frefedSequence.add(new Object[] { dsfor, jmap });
+ frefedSequence.add(newMappingRef(dsfor, jmap));
}
}
else
djs.setEnd(jmap.getMap().getToHighest());
djs.setVamsasId(uniqueSetSuffix + sqid);
jmap.setTo(djs);
+ incompleteSeqs.put(sqid, djs);
seqRefIds.put(sqid, djs);
}
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
import jalview.fts.service.pdb.PDBFTSRestClient;
+import jalview.io.DataSourceType;
import jalview.jbgui.GStructureChooser;
+import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.ws.DBRefFetcher;
+import jalview.ws.phyre2.Phyre2Client;
+import jalview.ws.phyre2.Phyre2SummaryPojo;
import jalview.ws.sifts.SiftsSettings;
import java.awt.event.ItemEvent;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Objects;
+import java.util.Set;
import java.util.Vector;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JLabel;
-import javax.swing.JOptionPane;
import javax.swing.table.AbstractTableModel;
/**
public class StructureChooser extends GStructureChooser implements
IProgressIndicator
{
- private boolean structuresDiscovered = false;
+ private static int MAX_QLENGTH = 7820;
private SequenceI selectedSequence;
private FTSRestClientI pdbRestCleint;
- private String selectedPdbFileName;
+ private String selectedStructureFileName;
private boolean isValidPBDEntry;
+ private boolean cachedPDBExists;
+
public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
AlignmentPanel ap)
{
progressBar = new ProgressBar(this.statusPanel, this.statusBar);
}
+ // ensure a filter option is in force for search
+ populateFilterComboBox(true, cachedPDBExists);
Thread discoverPDBStructuresThread = new Thread(new Runnable()
{
@Override
.getString("status.searching_for_pdb_structures"),
startTime);
fetchStructuresMetaData();
- populateFilterComboBox();
+ // revise filter options if no results were found
+ populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists);
updateProgressIndicator(null, startTime);
mainFrame.setVisible(true);
updateCurrentView();
pdbRequest.setAllowEmptySeq(false);
pdbRequest.setResponseSize(500);
pdbRequest.setFieldToSearchBy("(");
+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+ .getSelectedItem());
+ pdbRequest.setFieldToSortBy(selectedFilterOpt.getValue(),
+ !chk_invertFilter.isSelected());
pdbRequest.setWantedFields(wantedFields);
pdbRequest.setSearchTerm(buildQuery(seq) + ")");
pdbRequest.setAssociatedSequence(seq);
&& !discoveredStructuresSet.isEmpty())
{
getResultTable().setModel(
- FTSRestResponse.getTableModel(lastPdbRequest,
- discoveredStructuresSet));
- structuresDiscovered = true;
+ JvSummaryTable.getTableModel(lastPdbRequest,
+ discoveredStructuresSet));
noOfStructuresFound = discoveredStructuresSet.size();
mainFrame.setTitle(MessageManager.formatMessage(
"label.structure_chooser_no_of_structures",
{
errorMsg.append(error).append("\n");
}
- JOptionPane.showMessageDialog(this, errorMsg.toString(),
+ JvOptionPane.showMessageDialog(this, errorMsg.toString(),
MessageManager.getString("label.pdb_web-service_error"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
}
}
}
}
}
}
-
+ cachedPDBExists = !entries.isEmpty();
PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries);
tbl_local_pdb.setModel(tableModelx);
}
boolean isPDBRefsFound = false;
boolean isUniProtRefsFound = false;
StringBuilder queryBuilder = new StringBuilder();
- HashSet<String> seqRefs = new LinkedHashSet<String>();
+ Set<String> seqRefs = new LinkedHashSet<String>();
- if (seq.getAllPDBEntries() != null)
+ if (seq.getAllPDBEntries() != null
+ && queryBuilder.length() < MAX_QLENGTH)
{
for (PDBEntry entry : seq.getAllPDBEntries())
{
if (isValidSeqName(entry.getId()))
{
- queryBuilder.append("pdb_id")
- .append(":")
-.append(entry.getId().toLowerCase())
- .append(" OR ");
+ queryBuilder.append("pdb_id:")
+ .append(entry.getId().toLowerCase()).append(" OR ");
isPDBRefsFound = true;
- // seqRefs.add(entry.getId());
}
}
}
{
for (DBRefEntry dbRef : seq.getDBRefs())
{
- if (isValidSeqName(getDBRefId(dbRef)))
+ if (isValidSeqName(getDBRefId(dbRef))
+ && queryBuilder.length() < MAX_QLENGTH)
{
if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
{
- queryBuilder
-.append("uniprot_accession").append(":")
- .append(getDBRefId(dbRef))
- .append(" OR ");
- queryBuilder
-.append("uniprot_id")
- .append(":")
+ queryBuilder.append("uniprot_accession:")
.append(getDBRefId(dbRef)).append(" OR ");
+ queryBuilder.append("uniprot_id:").append(getDBRefId(dbRef))
+ .append(" OR ");
isUniProtRefsFound = true;
}
else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
{
- queryBuilder.append("pdb_id")
- .append(":").append(getDBRefId(dbRef).toLowerCase())
- .append(" OR ");
+ queryBuilder.append("pdb_id:")
+ .append(getDBRefId(dbRef).toLowerCase()).append(" OR ");
isPDBRefsFound = true;
}
else
.replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+");
}
-
/**
* Ensures sequence ref names are not less than 3 characters and does not
* contain a database name
reorderedStructuresSet.addAll(filteredResponse);
reorderedStructuresSet.addAll(discoveredStructuresSet);
getResultTable().setModel(
- FTSRestResponse.getTableModel(
- lastPdbRequest, reorderedStructuresSet));
+ JvSummaryTable.getTableModel(lastPdbRequest,
+ reorderedStructuresSet));
- FTSRestResponse.configureTableColumn(getResultTable(),
- wantedFields);
+ JvSummaryTable.configureTableColumn(getResultTable(),
+ wantedFields, tempUserPrefs);
getResultTable().getColumn("Ref Sequence").setPreferredWidth(120);
getResultTable().getColumn("Ref Sequence").setMinWidth(100);
getResultTable().getColumn("Ref Sequence").setMaxWidth(200);
{
errorMsg.append(error).append("\n");
}
- JOptionPane.showMessageDialog(
+ JvOptionPane.showMessageDialog(
null,
errorMsg.toString(),
MessageManager.getString("label.pdb_web-service_error"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
}
}
int value = chooser.showOpenDialog(null);
if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
{
- selectedPdbFileName = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
+ selectedStructureFileName = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedStructureFileName);
validateSelections();
}
}
* Populates the filter combo-box options dynamically depending on discovered
* structures
*/
- @Override
- protected void populateFilterComboBox()
+ protected void populateFilterComboBox(boolean haveData,
+ boolean cachedPDBExists)
{
- if (isStructuresDiscovered())
+ /*
+ * temporarily suspend the change listener behaviour
+ */
+ cmb_filterOption.removeItemListener(this);
+
+ cmb_filterOption.removeAllItems();
+ if (haveData)
{
cmb_filterOption.addItem(new FilterOption("Best Quality",
- "overall_quality", VIEWS_FILTER));
+ "overall_quality", VIEWS_FILTER, false));
cmb_filterOption.addItem(new FilterOption("Best Resolution",
- "resolution", VIEWS_FILTER));
+ "resolution", VIEWS_FILTER, false));
cmb_filterOption.addItem(new FilterOption("Most Protein Chain",
- "number_of_protein_chains", VIEWS_FILTER));
+ "number_of_protein_chains", VIEWS_FILTER, false));
cmb_filterOption.addItem(new FilterOption("Most Bound Molecules",
- "number_of_bound_molecules", VIEWS_FILTER));
+ "number_of_bound_molecules", VIEWS_FILTER, false));
cmb_filterOption.addItem(new FilterOption("Most Polymer Residues",
- "number_of_polymer_residues", VIEWS_FILTER));
+ "number_of_polymer_residues", VIEWS_FILTER, true));
}
cmb_filterOption.addItem(new FilterOption("Enter PDB Id", "-",
- VIEWS_ENTER_ID));
+ VIEWS_ENTER_ID, false));
cmb_filterOption.addItem(new FilterOption("From File", "-",
- VIEWS_FROM_FILE));
- cmb_filterOption.addItem(new FilterOption("Cached PDB Entries", "-",
- VIEWS_LOCAL_PDB));
+ VIEWS_FROM_FILE, false));
+
+ if (cachedPDBExists)
+ {
+ FilterOption cachedOption = new FilterOption("Cached PDB Entries",
+ "-", VIEWS_LOCAL_PDB, false);
+ cmb_filterOption.addItem(cachedOption);
+ cmb_filterOption.setSelectedItem(cachedOption);
+ }
+
+ cmb_filterOption.addItem(new FilterOption(
+ "Predict 3D Model with Phyre2", "-", VIEWS_PHYRE2_PREDICTION,
+ false));
+ cmb_filterOption.addItemListener(this);
}
/**
* Updates the displayed view based on the selected filter option
*/
- @Override
protected void updateCurrentView()
{
FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
chk_invertFilter.setVisible(true);
filterResultSet(selectedFilterOpt.getValue());
}
+ else if (selectedFilterOpt.getView() == VIEWS_PHYRE2_PREDICTION)
+ {
+ mainFrame.setTitle(MessageManager
+ .getString("label.phyre2_model_prediction"));
+ phyre2InputAssSeqPanel.loadCmbAssSeq();
+ }
else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
|| selectedFilterOpt.getView() == VIEWS_FROM_FILE)
{
{
validateAssociationFromFile();
}
+ else if (currentView == VIEWS_PHYRE2_PREDICTION)
+ {
+ validateAssociationFromPhyre2();
+ if (getPhyreResultTable().getSelectedRows().length > 0)
+ {
+ btn_view.setEnabled(true);
+ }
+ }
}
/**
"-Select Associated Seq-")))
{
btn_pdbFromFile.setEnabled(true);
- if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
+ if (selectedStructureFileName != null && selectedStructureFileName.length() > 0)
{
btn_view.setEnabled(true);
lbl_fromFileStatus.setIcon(goodImage);
}
}
+ /**
+ * Validates inputs for Phyre2 3D Model prediction
+ */
+ public void validateAssociationFromPhyre2()
+ {
+ AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) phyre2InputAssSeqPanel
+ .getCmb_assSeq().getSelectedItem();
+ if (selectedSequences.length == 1
+ || (assSeqOpt != null && !assSeqOpt.getName().equalsIgnoreCase(
+ "-Select Associated Seq-")))
+ {
+ btn_runPhyre2Prediction.setEnabled(true);
+ }
+ else
+ {
+ btn_runPhyre2Prediction.setEnabled(false);
+ }
+ }
+
@Override
public void cmbAssSeqStateChanged()
{
@Override
public void ok_ActionPerformed()
{
- final long progressSessionId = System.currentTimeMillis();
final StructureSelectionManager ssm = ap.getStructureSelectionManager();
+ final int preferredHeight = pnl_filter.getHeight();
- ssm.setProgressIndicator(this);
- ssm.setProgressSessionId(progressSessionId);
+ ssm.setMappingForPhyre2Model(false);
new Thread(new Runnable()
{
@Override
public void run()
{
- FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
- .getSelectedItem());
- String currentView = selectedFilterOpt.getView();
- if (currentView == VIEWS_FILTER)
- {
+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+ .getSelectedItem());
+ String currentView = selectedFilterOpt.getView();
+ if (currentView == VIEWS_FILTER)
+ {
int pdbIdColIndex = getResultTable().getColumn("PDB Id")
.getModelIndex();
int refSeqColIndex = getResultTable().getColumn("Ref Sequence")
- .getModelIndex();
+ .getModelIndex();
int[] selectedRows = getResultTable().getSelectedRows();
- PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
- int count = 0;
- ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
- for (int row : selectedRows)
- {
+ PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
+ int count = 0;
+ List<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
+ for (int row : selectedRows)
+ {
String pdbIdStr = getResultTable().getValueAt(row,
- pdbIdColIndex)
- .toString();
+ pdbIdColIndex).toString();
SequenceI selectedSeq = (SequenceI) getResultTable()
- .getValueAt(row,
- refSeqColIndex);
- selectedSeqsToView.add(selectedSeq);
+ .getValueAt(row, refSeqColIndex);
+ selectedSeqsToView.add(selectedSeq);
PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
if (pdbEntry == null)
{
pdbEntry = getFindEntry(pdbIdStr,
selectedSeq.getAllPDBEntries());
}
- if (pdbEntry == null)
- {
- pdbEntry = new PDBEntry();
- pdbEntry.setId(pdbIdStr);
- pdbEntry.setType(PDBEntry.Type.PDB);
- selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
+ if (pdbEntry == null)
+ {
+ pdbEntry = new PDBEntry();
+ pdbEntry.setId(pdbIdStr);
+ pdbEntry.setType(PDBEntry.Type.PDB);
+ selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
+ }
+ pdbEntriesToView[count++] = pdbEntry;
+ }
+ SequenceI[] selectedSeqs = selectedSeqsToView
+ .toArray(new SequenceI[selectedSeqsToView.size()]);
+ launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
}
- pdbEntriesToView[count++] = pdbEntry;
- }
- SequenceI[] selectedSeqs = selectedSeqsToView
- .toArray(new SequenceI[selectedSeqsToView.size()]);
- launchStructureViewer(ssm, pdbEntriesToView, ap,
- selectedSeqs);
- }
- else if (currentView == VIEWS_LOCAL_PDB)
- {
- int[] selectedRows = tbl_local_pdb.getSelectedRows();
- PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
- int count = 0;
+ else if (currentView == VIEWS_LOCAL_PDB)
+ {
+ int[] selectedRows = tbl_local_pdb.getSelectedRows();
+ PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
+ int count = 0;
int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id")
.getModelIndex();
- int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
- .getModelIndex();
- ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
- for (int row : selectedRows)
- {
- PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
- pdbIdColIndex);
- pdbEntriesToView[count++] = pdbEntry;
- SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt(row,
- refSeqColIndex);
- selectedSeqsToView.add(selectedSeq);
- }
- SequenceI[] selectedSeqs = selectedSeqsToView
- .toArray(new SequenceI[selectedSeqsToView.size()]);
- launchStructureViewer(ssm, pdbEntriesToView, ap,
- selectedSeqs);
- }
- else if (currentView == VIEWS_ENTER_ID)
- {
- SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
- .getCmb_assSeq().getSelectedItem()).getSequence();
- if (userSelectedSeq != null)
- {
- selectedSequence = userSelectedSeq;
- }
+ int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
+ .getModelIndex();
+ List<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
+ for (int row : selectedRows)
+ {
+ PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
+ pdbIdColIndex);
+ pdbEntriesToView[count++] = pdbEntry;
+ SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt(
+ row, refSeqColIndex);
+ selectedSeqsToView.add(selectedSeq);
+ }
+ SequenceI[] selectedSeqs = selectedSeqsToView
+ .toArray(new SequenceI[selectedSeqsToView.size()]);
+ launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
+ }
+ else if (currentView == VIEWS_ENTER_ID)
+ {
+ SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
+ .getCmb_assSeq().getSelectedItem()).getSequence();
+ if (userSelectedSeq != null)
+ {
+ selectedSequence = userSelectedSeq;
+ }
- String pdbIdStr = txt_search.getText();
- PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
- if (pdbEntry == null)
- {
- pdbEntry = new PDBEntry();
++
+ String pdbIdStr = txt_search.getText();
+ PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
+ if (pdbEntry == null)
+ {
+ pdbEntry = new PDBEntry();
if (pdbIdStr.split(":").length > 1)
{
- pdbEntry.setChainCode(pdbIdStr.split(":")[1]);
+ pdbEntry.setId(pdbIdStr.split(":")[0]);
+ pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase());
}
- pdbEntry.setId(pdbIdStr);
- pdbEntry.setType(PDBEntry.Type.PDB);
- selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
- }
+ else
+ {
+ pdbEntry.setId(pdbIdStr);
+ }
+ pdbEntry.setType(PDBEntry.Type.PDB);
+ selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
+ }
- PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
+ PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
launchStructureViewer(ssm, pdbEntriesToView, ap,
new SequenceI[] { selectedSequence });
}
{
selectedSequence = userSelectedSeq;
}
- PDBEntry fileEntry = new AssociatePdbFileWithSeq()
- .associatePdbWithSeq(selectedPdbFileName,
- jalview.io.AppletFormatAdapter.FILE,
+ PDBEntry fileEntry = new AssociateStructureFileWithSeq()
+ .associateStructureWithSeq(selectedStructureFileName,
+ DataSourceType.FILE,
selectedSequence, true, Desktop.instance);
- launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
+ launchStructureViewer(ssm,
+ new PDBEntry[] { fileEntry }, ap,
new SequenceI[] { selectedSequence });
- }
- mainFrame.dispose();
+ }
+ else if (currentView == VIEWS_PHYRE2_PREDICTION)
+ {
+ SequenceI userSelectedSeq = ((AssociateSeqOptions) phyre2InputAssSeqPanel
+ .getCmb_assSeq().getSelectedItem()).getSequence();
+ if (userSelectedSeq != null)
+ {
+ selectedSequence = userSelectedSeq;
+ }
+ int templateColIndex = getPhyreResultTable()
+ .getColumn("Template")
+ .getModelIndex();
+ int[] selectedRows = getPhyreResultTable().getSelectedRows();
+ PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
+ int count = 0;
+ for (int row : selectedRows)
+ {
+ String templateId = getPhyreResultTable().getValueAt(row,
+ templateColIndex).toString();
+ String structureFile = phyre2ResultDirectory + templateId
+ + ".pdb";
+ pdbEntriesToView[count++] = new AssociateStructureFileWithSeq()
+ .associateStructureWithSeq(structureFile,
+ DataSourceType.FILE, selectedSequence, true,
+ Desktop.instance);
+ }
+
+ final StructureSelectionManager ssm = ap
+ .getStructureSelectionManager();
+ ssm.setMappingForPhyre2Model(true);
+ final long progressSessionId = System.currentTimeMillis();
+ ssm.setProgressSessionId(progressSessionId);
+
+ SequenceI[] sequences = new SequenceI[] { selectedSequence };
+
+ ssm.setProgressBar(MessageManager
+ .getString("status.launching_3d_structure_viewer"));
+ final StructureViewer sViewer = new StructureViewer(ssm);
+ if (pdbEntriesToView.length > 1)
+ {
+ ArrayList<SequenceI[]> seqsMap = new ArrayList<SequenceI[]>();
+ for (SequenceI seq : sequences)
+ {
+ seqsMap.add(new SequenceI[] { seq });
+ }
+ SequenceI[][] collatedSeqs = seqsMap
+ .toArray(new SequenceI[0][0]);
+ ssm.setProgressBar(null);
+ ssm.setProgressBar(MessageManager
+ .getString("status.fetching_3d_structures_for_selected_entries"));
+ sViewer.viewStructures(pdbEntriesToView, collatedSeqs, ap);
+ }
+ else
+ {
+ ssm.setProgressBar(null);
+ ssm.setProgressBar(MessageManager.formatMessage(
+ "status.fetching_3d_structures_for",
+ pdbEntriesToView[0].getId()));
+ sViewer.viewStructures(pdbEntriesToView[0], sequences, ap);
+ }
+ }
+ closeAction(preferredHeight);
}
}).start();
}
+ private String phyre2ResultDirectory;
+
+ @Override
+ public void predict3DModelWithPhyre2()
+ {
+ // TODO implement code for submitting sequence to Phyre2 service, and code
+ // for getting the result directory when the job completes, this is
+ // currently hard-wired to the directory of result for FER_CAPAN/1-144
+ phyre2ResultDirectory = "examples/testdata/phyre2results/56da5616b4559c93/";
+ String summaryhtml = phyre2ResultDirectory + "summary.html";
+ // TODO ditch HTML parsing once appropriated data file (i.e. JSON) for
+ // Phyre2 result summary is made available
+ List<Phyre2SummaryPojo> phyreResults = Phyre2Client
+ .parsePhyre2ResultSummaryTable(summaryhtml);
+ getPhyreResultTable()
+ .setModel(Phyre2Client.getTableModel(phyreResults));
+ Phyre2Client.configurePhyreResultTable(getPhyreResultTable());
+ }
+
private PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
{
Objects.requireNonNull(id);
final PDBEntry[] pdbEntriesToView,
final AlignmentPanel alignPanel, SequenceI[] sequences)
{
- ssm.setProgressBar(MessageManager
- .getString("status.launching_3d_structure_viewer"));
+ long progressId = sequences.hashCode();
+ setProgressBar(MessageManager
+ .getString("status.launching_3d_structure_viewer"), progressId);
final StructureViewer sViewer = new StructureViewer(ssm);
+ setProgressBar(null, progressId);
if (SiftsSettings.isMapWithSifts())
{
- // TODO: prompt user if there are lots of sequences without dbrefs.
- // It can take a long time if we need to fetch all dbrefs for all
- // sequences!
- ArrayList<SequenceI> seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
+ List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
+ int p = 0;
+ // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a
+ // real PDB ID. For moment, we can also safely do this if there is already
+ // a known mapping between the PDBEntry and the sequence.
++
for (SequenceI seq : sequences)
{
- if (seq.getSourceDBRef() == null && seq.getDBRefs() == null)
+ PDBEntry pdbe = pdbEntriesToView[p++];
+ if (pdbe != null && pdbe.getFile() != null)
{
- seqsWithoutSourceDBRef.add(seq);
- continue;
+ StructureMapping[] smm = ssm.getMapping(pdbe.getFile());
+ if (smm != null && smm.length > 0)
+ {
+ for (StructureMapping sm : smm)
+ {
+ if (sm.getSequence() == seq)
+ {
+ continue;
+ }
+ }
}
+ }
+ if (seq.getPrimaryDBRefs().size() == 0)
+ {
+ seqsWithoutSourceDBRef.add(seq);
+ continue;
+ }
}
if (!seqsWithoutSourceDBRef.isEmpty())
{
int y = seqsWithoutSourceDBRef.size();
- ssm.setProgressBar(null);
- ssm.setProgressBar(MessageManager.formatMessage(
+ setProgressBar(MessageManager.formatMessage(
"status.fetching_dbrefs_for_sequences_without_valid_refs",
- y));
+ y), progressId);
SequenceI[] seqWithoutSrcDBRef = new SequenceI[y];
int x = 0;
for (SequenceI fSeq : seqsWithoutSourceDBRef)
{
seqWithoutSrcDBRef[x++] = fSeq;
}
- DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
- dbRefFetcher.fetchDBRefs(true);
+ new DBRefFetcher(seqWithoutSrcDBRef).fetchDBRefs(true);
+ setProgressBar("Fetch complete.", progressId); // todo i18n
}
}
if (pdbEntriesToView.length > 1)
seqsMap.add(new SequenceI[] { seq });
}
SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]);
- ssm.setProgressBar(null);
- ssm.setProgressBar(MessageManager
- .getString("status.fetching_3d_structures_for_selected_entries"));
+ setProgressBar(MessageManager
+ .getString("status.fetching_3d_structures_for_selected_entries"), progressId);
sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel);
}
else
{
- ssm.setProgressBar(null);
- ssm.setProgressBar(MessageManager.formatMessage(
+ setProgressBar(MessageManager.formatMessage(
"status.fetching_3d_structures_for",
- pdbEntriesToView[0].getId()));
+ pdbEntriesToView[0].getId()),progressId);
sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
}
+ setProgressBar(null, progressId);
}
/**
public boolean isStructuresDiscovered()
{
- return structuresDiscovered;
- }
-
- public void setStructuresDiscovered(boolean structuresDiscovered)
- {
- this.structuresDiscovered = structuresDiscovered;
+ return discoveredStructuresSet != null
+ && !discoveredStructuresSet.isEmpty();
}
public Collection<FTSData> getDiscoveredStructuresSet()
pdbRequest.setResponseSize(1);
pdbRequest.setFieldToSearchBy("(pdb_id:");
pdbRequest.setWantedFields(wantedFields);
- pdbRequest
-.setSearchTerm(searchTerm + ")");
+ pdbRequest.setSearchTerm(searchTerm + ")");
pdbRequest.setAssociatedSequence(selectedSequence);
pdbRestCleint = PDBFTSRestClient.getInstance();
wantedFields.add(pdbRestCleint.getPrimaryKeyColumn());
import jalview.datamodel.SequenceI;
import jalview.gui.StructureViewer.ViewerType;
import jalview.gui.ViewSelectionMenu.ViewSetProvider;
-import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
import jalview.jbgui.GStructureViewer;
import jalview.structures.models.AAStructureBindingModel;
import jalview.util.MessageManager;
import java.awt.Component;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
import java.util.ArrayList;
import java.util.List;
import java.util.Vector;
+import javax.swing.JCheckBoxMenuItem;
import javax.swing.JMenuItem;
--import javax.swing.JOptionPane;
/**
* Base class with common functionality for JMol, Chimera or other structure
protected Thread worker = null;
+ protected boolean allChainsSelected = false;
+
/**
*
* @param ap2
protected abstract AAStructureBindingModel getBindingModel();
+ protected abstract IProgressIndicator getIProgressIndicator();
+
/**
* add a new structure (with associated sequences and chains) to this viewer,
* retrieving it if necessary first.
*
* @param pdbId
* @param view
- * @return YES, NO or CANCEL JOptionPane code
+ * @return YES, NO or CANCEL JvOptionPane code
*/
protected int chooseAlignStructureToViewer(String pdbId,
StructureViewerBase view)
{
- int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ int option = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
MessageManager.formatMessage("label.add_pdbentry_to_view",
new Object[] { pdbId, view.getTitle() }),
MessageManager
.getString("label.align_to_existing_structure_view"),
- JOptionPane.YES_NO_CANCEL_OPTION);
+ JvOptionPane.YES_NO_CANCEL_OPTION);
return option;
}
continue;
}
int option = chooseAlignStructureToViewer(pdbId, view);
- if (option == JOptionPane.CANCEL_OPTION)
+ if (option == JvOptionPane.CANCEL_OPTION)
{
return true;
}
- else if (option == JOptionPane.YES_OPTION)
+ else if (option == JvOptionPane.YES_OPTION)
{
view.useAlignmentPanelForSuperposition(apanel);
view.addStructure(pdbentry, seq, chains, true, apanel.alignFrame);
* create the mappings
*/
apanel.getStructureSelectionManager().setMapping(seq, chains,
- pdbFilename, DataSourceType.FILE);
- pdbFilename, AppletFormatAdapter.FILE, getIProgressIndicator());
++ pdbFilename, DataSourceType.FILE, getIProgressIndicator());
/*
* alert the FeatureRenderer to show new (PDB RESNUM) features
/*
* the PDB file is already loaded
*/
- int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ int option = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
MessageManager.formatMessage(
"label.pdb_entry_is_already_displayed",
new Object[] { pdbId }), MessageManager
.formatMessage(
"label.map_sequences_to_visible_window",
new Object[] { pdbId }),
- JOptionPane.YES_NO_CANCEL_OPTION);
- if (option == JOptionPane.CANCEL_OPTION)
+ JvOptionPane.YES_NO_CANCEL_OPTION);
+ if (option == JvOptionPane.CANCEL_OPTION)
{
finished = true;
}
- else if (option == JOptionPane.YES_OPTION)
+ else if (option == JvOptionPane.YES_OPTION)
{
addSequenceMappingsToStructure(seq, chains, apanel, alreadyMapped);
finished = true;
}
return finished;
}
+
+ void setChainMenuItems(List<String> chainNames)
+ {
+ chainMenu.removeAll();
+ if (chainNames == null || chainNames.isEmpty())
+ {
+ return;
+ }
+ JMenuItem menuItem = new JMenuItem(
+ MessageManager.getString("label.all"));
+ menuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent evt)
+ {
+ allChainsSelected = true;
+ for (int i = 0; i < chainMenu.getItemCount(); i++)
+ {
+ if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
+ {
+ ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
+ }
+ }
+ showSelectedChains();
+ allChainsSelected = false;
+ }
+ });
+
+ chainMenu.add(menuItem);
+
+ for (String chain : chainNames)
+ {
+ menuItem = new JCheckBoxMenuItem(chain, true);
+ menuItem.addItemListener(new ItemListener()
+ {
+ @Override
+ public void itemStateChanged(ItemEvent evt)
+ {
+ if (!allChainsSelected)
+ {
+ showSelectedChains();
+ }
+ }
+ });
+
+ chainMenu.add(menuItem);
+ }
+ }
+
+ abstract void showSelectedChains();
+
}
import jalview.datamodel.Annotation;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JmolParser;
import jalview.gui.IProgressIndicator;
-import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
import jalview.io.StructureFile;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
+import jalview.ws.phyre2.Phyre2Client;
import jalview.ws.sifts.SiftsClient;
import jalview.ws.sifts.SiftsException;
import jalview.ws.sifts.SiftsSettings;
private boolean addTempFacAnnot = false;
+ private IProgressIndicator progressIndicator;
+
private SiftsClient siftsClient = null;
+ private long progressSessionId;
+
+ private boolean mappingForPhyre2Model;
+
/*
* Set of any registered mappings between (dataset) sequences.
*/
* @return null or the structure data parsed as a pdb file
*/
synchronized public StructureFile setMapping(SequenceI[] sequence,
- String[] targetChains, String pdbFile, DataSourceType protocol)
- String[] targetChains, String pdbFile, String protocol,
++ String[] targetChains, String pdbFile, DataSourceType protocol,
+ IProgressIndicator progress)
{
- return setMapping(true, sequence, targetChains, pdbFile, protocol);
+ return computeMapping(true, sequence, targetChains, pdbFile, protocol,
+ progress);
}
+
/**
* create sequence structure mappings between each sequence and the given
* pdbFile (retrieved via the given protocol).
* - one or more sequences to be mapped to pdbFile
* @param targetChainIds
* - optional chain specification for mapping each sequence to pdb
- * (may be nill, individual elements may be nill)
+ * (may be null, individual elements may be null)
* @param pdbFile
* - structure data resource
- * @param sourceType
+ * @param protocol
* - how to resolve data from resource
* @return null or the structure data parsed as a pdb file
*/
synchronized public StructureFile setMapping(boolean forStructureView,
SequenceI[] sequenceArray, String[] targetChainIds,
- String pdbFile, DataSourceType sourceType)
- String pdbFile,
- String protocol)
++ String pdbFile, DataSourceType protocol)
{
+ return computeMapping(forStructureView, sequenceArray, targetChainIds,
+ pdbFile, protocol, null);
+ }
+
+ synchronized public StructureFile computeMapping(
+ boolean forStructureView, SequenceI[] sequenceArray,
- String[] targetChainIds, String pdbFile, String protocol,
++ String[] targetChainIds, String pdbFile, DataSourceType protocol,
+ IProgressIndicator progress)
+ {
+ long progressSessionId = System.currentTimeMillis() * 3;
/*
* There will be better ways of doing this in the future, for now we'll use
* the tried and tested MCview pdb mapping
boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
try
{
- pdb = new JmolParser(pdbFile, sourceType);
-
- if (pdbFile != null && isCIFFile(pdbFile))
- {
- pdb = new jalview.ext.jmol.JmolParser(addTempFacAnnot, parseSecStr,
- secStructServices, pdbFile, protocol);
- }
- else
- {
- pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices,
- pdbFile, protocol);
- }
++ pdb = new JmolParser(pdbFile, protocol);
if (pdb.getId() != null && pdb.getId().trim().length() > 0
- && DataSourceType.FILE == sourceType)
- && AppletFormatAdapter.FILE.equals(protocol))
++ && DataSourceType.FILE == protocol)
{
registerPDBFile(pdb.getId().trim(), pdbFile);
}
+ // if PDBId is unavailable then skip SIFTS mapping execution path
+ isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable();
+
} catch (Exception ex)
{
ex.printStackTrace();
{
boolean infChain = true;
final SequenceI seq = sequenceArray[s];
+ SequenceI ds = seq;
+ while (ds.getDatasetSequence() != null)
+ {
+ ds = ds.getDatasetSequence();
+ }
+
if (targetChainIds != null && targetChainIds[s] != null)
{
infChain = false;
continue;
}
- if (sourceType == DataSourceType.PASTE)
- if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
++ if (protocol.equals(DataSourceType.PASTE))
{
pdbFile = "INLINE" + pdb.getId();
}
- ArrayList<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
- if (isMapUsingSIFTs)
+
+ List<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
+ if (!isMappingForPhyre2Model() && isMapUsingSIFTs && seq.isProtein())
{
- setProgressBar(null);
- setProgressBar(MessageManager
- .getString("status.obtaining_mapping_with_sifts"));
+ if (progress!=null) {
+ progress.setProgressBar(MessageManager
+ .getString("status.obtaining_mapping_with_sifts"),
+ progressSessionId);
+ }
jalview.datamodel.Mapping sqmpping = maxAlignseq
.getMappingFromS1(false);
if (targetChainId != null && !targetChainId.trim().isEmpty())
pdb, maxChain, sqmpping, maxAlignseq);
seqToStrucMapping.add(siftsMapping);
maxChain.makeExactMapping(maxAlignseq, seq);
- maxChain.transferRESNUMFeatures(seq, null);
+ maxChain.transferRESNUMFeatures(seq, null);// FIXME: is this
+ // "IEA:SIFTS" ?
maxChain.transferResidueAnnotation(siftsMapping, sqmpping);
+ ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
+
} catch (SiftsException e)
{
// fall back to NW alignment
StructureMapping nwMapping = getNWMappings(seq, pdbFile,
targetChainId, maxChain, pdb, maxAlignseq);
seqToStrucMapping.add(nwMapping);
+ maxChain.makeExactMapping(maxAlignseq, seq);
+ maxChain.transferRESNUMFeatures(seq, null); // FIXME: is this
+ // "IEA:Jalview" ?
+ maxChain.transferResidueAnnotation(nwMapping, sqmpping);
+ ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
+ } catch (Exception e)
+ {
+ e.printStackTrace();
}
}
else
{
- ArrayList<StructureMapping> foundSiftsMappings = new ArrayList<StructureMapping>();
+ List<StructureMapping> foundSiftsMappings = new ArrayList<StructureMapping>();
for (PDBChain chain : pdb.getChains())
{
try
{
StructureMapping siftsMapping = getStructureMapping(seq,
- pdbFile,
- chain.id, pdb, chain, sqmpping, maxAlignseq);
+ pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq);
foundSiftsMappings.add(siftsMapping);
} catch (SiftsException e)
{
System.err.println(e.getMessage());
+ } catch (Exception e)
+ {
+ e.printStackTrace();
}
}
if (!foundSiftsMappings.isEmpty())
{
seqToStrucMapping.addAll(foundSiftsMappings);
maxChain.makeExactMapping(maxAlignseq, seq);
- maxChain.transferRESNUMFeatures(seq, null);
+ maxChain.transferRESNUMFeatures(seq, null);// FIXME: is this
+ // "IEA:SIFTS" ?
maxChain.transferResidueAnnotation(foundSiftsMappings.get(0),
sqmpping);
+ ds.addPDBId(sqmpping.getTo().getAllPDBEntries().get(0));
}
else
{
StructureMapping nwMapping = getNWMappings(seq, pdbFile,
maxChainId, maxChain, pdb, maxAlignseq);
seqToStrucMapping.add(nwMapping);
+ maxChain.transferRESNUMFeatures(seq, null); // FIXME: is this
+ // "IEA:Jalview" ?
+ maxChain.transferResidueAnnotation(nwMapping, sqmpping);
+ ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
}
}
}
+ else if (isMappingForPhyre2Model())
+ {
+ setProgressBar(null);
+ setProgressBar(MessageManager
+ .getString("status.obtaining_mapping_with_phyre2_template_alignment"));
+ StructureMapping phyre2ModelMapping = new Phyre2Client(pdb)
+ .getStructureMapping(seq, pdbFile, " ");
+
+ seqToStrucMapping.add(phyre2ModelMapping);
+ ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
+ }
else
{
- setProgressBar(null);
- setProgressBar(MessageManager
- .getString("status.obtaining_mapping_with_nw_alignment"));
+ if (progress != null)
+ {
+ progress.setProgressBar(MessageManager
- .getString("status.obtaining_mapping_with_nw_alignment"),
++ .getString("status.obtaining_mapping_with_nw_alignment"),
+ progressSessionId);
+ }
- seqToStrucMapping.add(getNWMappings(seq, pdbFile, maxChainId,
- maxChain, pdb, maxAlignseq));
+ StructureMapping nwMapping = getNWMappings(seq, pdbFile,
+ maxChainId, maxChain, pdb, maxAlignseq);
+ seqToStrucMapping.add(nwMapping);
+ ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
+
}
+
if (forStructureView)
{
mappings.addAll(seqToStrucMapping);
}
- if (progress != null)
- {
- progress.setProgressBar(null, progressSessionId);
- }
}
return pdb;
}
return "cif".equalsIgnoreCase(fileExt);
}
+ /**
+ * retrieve a mapping for seq from SIFTs using associated DBRefEntry for
+ * uniprot or PDB
+ *
+ * @param seq
+ * @param pdbFile
+ * @param targetChainId
+ * @param pdb
+ * @param maxChain
+ * @param sqmpping
+ * @param maxAlignseq
+ * @return
+ * @throws SiftsException
+ */
private StructureMapping getStructureMapping(SequenceI seq,
String pdbFile, String targetChainId, StructureFile pdb,
PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
- AlignSeq maxAlignseq) throws SiftsException
+ AlignSeq maxAlignseq) throws Exception
{
- StructureMapping curChainMapping = siftsClient
- .getSiftsStructureMapping(seq, pdbFile, targetChainId);
- try
- {
+ StructureMapping curChainMapping = siftsClient
+ .getStructureMapping(seq, pdbFile, targetChainId);
+ try
+ {
PDBChain chain = pdb.findChain(targetChainId);
if (chain != null)
{
chain.transferResidueAnnotation(curChainMapping, sqmpping);
}
- } catch (Exception e)
- {
- e.printStackTrace();
- }
- return curChainMapping;
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ return curChainMapping;
}
- private StructureMapping getNWMappings(SequenceI seq,
- String pdbFile,
+ private StructureMapping getNWMappings(SequenceI seq, String pdbFile,
String maxChainId, PDBChain maxChain, StructureFile pdb,
AlignSeq maxAlignseq)
{
return;
}
- SearchResults results = new SearchResults();
+ SearchResultsI results = new SearchResults();
for (AtomSpec atom : atoms)
{
SequenceI lastseq = null;
{
boolean hasSequenceListeners = handlingVamsasMo
|| !seqmappings.isEmpty();
- SearchResults results = null;
+ SearchResultsI results = null;
if (seqPos == -1)
{
seqPos = seq.findPosition(indexpos);
return null;
}
+ public IProgressIndicator getProgressIndicator()
+ {
+ return progressIndicator;
+ }
+
+ public void setProgressIndicator(IProgressIndicator progressIndicator)
+ {
+ this.progressIndicator = progressIndicator;
+ }
+
+ public long getProgressSessionId()
+ {
+ return progressSessionId;
+ }
+
+ public void setProgressSessionId(long progressSessionId)
+ {
+ this.progressSessionId = progressSessionId;
+ }
+
+ public void setProgressBar(String message)
+ {
+ if (progressIndicator == null)
+ {
+ return;
+ }
+ progressIndicator.setProgressBar(message, progressSessionId);
+ }
+
public List<AlignedCodonFrame> getSequenceMappings()
{
return seqmappings;
}
+ public boolean isMappingForPhyre2Model()
+ {
+ return mappingForPhyre2Model;
+ }
+
+ public void setMappingForPhyre2Model(boolean mappingForPhyre2Model)
+ {
+ this.mappingForPhyre2Model = mappingForPhyre2Model;
+ }
+
+ public static StructureSelectionManager getStructureSelectionManager()
+ {
+ return instances.values().iterator().next();
+ }
+
}
import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
import jalview.structure.AtomSpec;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel.SuperposeData;
import java.util.Arrays;
import java.util.List;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
*/
public class AAStructureBindingModelTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ /*
+ * Scenario: Jalview has 4 sequences, corresponding to 1YCS (chains A and B), 3A6S|B, 1OOT|A
+ */
private static final String PDB_1 = "HEADER COMPLEX (ANTI-ONCOGENE/ANKYRIN REPEATS) 30-SEP-96 1YCS \n"
+ "ATOM 2 CA VAL A 97 24.134 4.926 45.821 1.00 47.43 C \n"
+ "ATOM 9 CA PRO A 98 25.135 8.584 46.217 1.00 41.60 C \n"
+ "ATOM 16 CA SER A 99 28.243 9.596 44.271 1.00 39.63 C \n"
+ "ATOM 22 CA GLN A 100 31.488 10.133 46.156 1.00 35.60 C \n"
- + "ATOM 31 CA LYS A 101 33.323 11.587 43.115 1.00 41.69 C \n";
+ // artificial jump in residue numbering to prove it is correctly
+ // mapped:
+ + "ATOM 31 CA LYS A 102 33.323 11.587 43.115 1.00 41.69 C \n"
+ + "ATOM 1857 CA GLU B 374 9.193 -16.005 95.870 1.00 54.22 C \n"
+ + "ATOM 1866 CA ILE B 375 7.101 -14.921 92.847 1.00 46.82 C \n"
+ + "ATOM 1874 CA VAL B 376 10.251 -13.625 91.155 1.00 47.80 C \n"
+ + "ATOM 1881 CA LYS B 377 11.767 -17.068 91.763 1.00 50.21 C \n"
+ + "ATOM 1890 CA PHE B 378 8.665 -18.948 90.632 1.00 44.85 C \n";
private static final String PDB_2 = "HEADER HYDROLASE 09-SEP-09 3A6S \n"
- + "ATOM 2 CA MET A 1 15.366 -11.648 24.854 1.00 32.05 C \n"
- + "ATOM 10 CA LYS A 2 16.846 -9.215 22.340 1.00 25.68 C \n"
- + "ATOM 19 CA LYS A 3 15.412 -6.335 20.343 1.00 19.42 C \n"
- + "ATOM 28 CA LEU A 4 15.629 -5.719 16.616 1.00 15.49 C \n"
- + "ATOM 36 CA GLN A 5 14.412 -2.295 15.567 1.00 12.19 C \n";
+ + "ATOM 2 CA MET B 1 15.366 -11.648 24.854 1.00 32.05 C \n"
+ + "ATOM 10 CA LYS B 2 16.846 -9.215 22.340 1.00 25.68 C \n"
+ + "ATOM 19 CA LYS B 3 15.412 -6.335 20.343 1.00 19.42 C \n"
+ + "ATOM 28 CA LEU B 4 15.629 -5.719 16.616 1.00 15.49 C \n"
+ + "ATOM 36 CA GLN B 5 14.412 -2.295 15.567 1.00 12.19 C \n";
private static final String PDB_3 = "HEADER STRUCTURAL GENOMICS 04-MAR-03 1OOT \n"
- + "ATOM 2 CA SER A 1 29.427 3.330 -6.578 1.00 32.50 C \n"
- + "ATOM 8 CA PRO A 2 29.975 3.340 -2.797 1.00 17.62 C \n"
- + "ATOM 16 CA ALYS A 3 26.958 3.024 -0.410 0.50 8.78 C \n"
- + "ATOM 33 CA ALA A 4 26.790 4.320 3.172 1.00 11.98 C \n"
- + "ATOM 39 CA AVAL A 5 24.424 3.853 6.106 0.50 13.83 C \n";
+ + "ATOM 2 CA SER A 7 29.427 3.330 -6.578 1.00 32.50 C \n"
+ + "ATOM 8 CA PRO A 8 29.975 3.340 -2.797 1.00 17.62 C \n"
+ + "ATOM 16 CA ALYS A 9 26.958 3.024 -0.410 0.50 8.78 C \n"
+ + "ATOM 33 CA ALA A 10 26.790 4.320 3.172 1.00 11.98 C \n"
+ + "ATOM 39 CA AVAL A 12 24.424 3.853 6.106 0.50 13.83 C \n";
AAStructureBindingModel testee;
@BeforeMethod(alwaysRun = true)
public void setUp()
{
- SequenceI seq1 = new Sequence("1YCS", "-VPSQK");
+ SequenceI seq1a = new Sequence("1YCS|A", "-VPSQK");
+ SequenceI seq1b = new Sequence("1YCS|B", "EIVKF-");
SequenceI seq2 = new Sequence("3A6S", "MK-KLQ");
SequenceI seq3 = new Sequence("1OOT", "SPK-AV");
- al = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
+ al = new Alignment(new SequenceI[] { seq1a, seq1b, seq2, seq3 });
al.setDataset(null);
+ /*
+ * give pdb files the name generated by Jalview for PASTE source
+ */
PDBEntry[] pdbFiles = new PDBEntry[3];
- pdbFiles[0] = new PDBEntry("1YCS", "A", Type.PDB, "1YCS.pdb");
- pdbFiles[1] = new PDBEntry("3A6S", "B", Type.PDB, "3A6S.pdb");
- pdbFiles[2] = new PDBEntry("1OOT", "A", Type.PDB, "1OOT.pdb");
- String[][] chains = new String[3][];
+ pdbFiles[0] = new PDBEntry("1YCS", "A", Type.PDB, "INLINE1YCS");
+ pdbFiles[1] = new PDBEntry("3A6S", "B", Type.PDB, "INLINE3A6S");
+ pdbFiles[2] = new PDBEntry("1OOT", "A", Type.PDB, "INLINE1OOT");
SequenceI[][] seqs = new SequenceI[3][];
- seqs[0] = new SequenceI[] { seq1 };
+ seqs[0] = new SequenceI[] { seq1a, seq1b };
seqs[1] = new SequenceI[] { seq2 };
seqs[2] = new SequenceI[] { seq3 };
StructureSelectionManager ssm = new StructureSelectionManager();
- ssm.setMapping(new SequenceI[] { seq1 }, null, PDB_1,
- AppletFormatAdapter.PASTE, null);
+ ssm.setMapping(new SequenceI[] { seq1a, seq1b }, null, PDB_1,
- DataSourceType.PASTE);
++ DataSourceType.PASTE, null);
ssm.setMapping(new SequenceI[] { seq2 }, null, PDB_2,
- DataSourceType.PASTE);
- AppletFormatAdapter.PASTE, null);
++ DataSourceType.PASTE, null);
ssm.setMapping(new SequenceI[] { seq3 }, null, PDB_3,
- DataSourceType.PASTE);
- AppletFormatAdapter.PASTE, null);
++ DataSourceType.PASTE, null);
++
- testee = new AAStructureBindingModel(ssm, pdbFiles, seqs, chains, null)
+ testee = new AAStructureBindingModel(ssm, pdbFiles, seqs, null)
{
@Override
public String[] getPdbFile()
{
- /*
- * fudge 'filenames' to match those generated when PDBFile parses PASTE
- * data
- */
return new String[] { "INLINE1YCS", "INLINE3A6S", "INLINE1OOT" };
}
public void highlightAtoms(List<AtomSpec> atoms)
{
}
+
+ @Override
+ public List<String> getChainNames()
+ {
+ return null;
+ }
};
}
@Test(groups = { "Functional" })
public void testFindSuperposableResidues()
{
- SuperposeData[] structs = new SuperposeData[al.getHeight()];
+ /*
+ * create a data bean to hold data per structure file
+ */
+ SuperposeData[] structs = new SuperposeData[testee.getPdbFile().length];
for (int i = 0; i < structs.length; i++)
{
structs[i] = testee.new SuperposeData(al.getWidth());
*/
assertFalse(matched[0]); // gap in first sequence
assertTrue(matched[1]);
- assertFalse(matched[2]); // gap in second sequence
- assertFalse(matched[3]); // gap in third sequence
+ assertFalse(matched[2]); // gap in third sequence
+ assertFalse(matched[3]); // gap in fourth sequence
assertTrue(matched[4]);
- assertTrue(matched[5]);
+ assertTrue(matched[5]); // gap in second sequence
+
+ assertEquals("1YCS", structs[0].pdbId);
+ assertEquals("3A6S", structs[1].pdbId);
+ assertEquals("1OOT", structs[2].pdbId);
+ assertEquals("A", structs[0].chain); // ? struct has chains A _and_ B
+ assertEquals("B", structs[1].chain);
+ assertEquals("A", structs[2].chain);
+ // the 0's for unsuperposable positions propagate down the columns:
+ assertEquals("[0, 97, 98, 99, 100, 102]",
+ Arrays.toString(structs[0].pdbResNo));
+ assertEquals("[0, 2, 0, 3, 4, 5]", Arrays.toString(structs[1].pdbResNo));
+ assertEquals("[0, 8, 0, 0, 10, 12]",
+ Arrays.toString(structs[2].pdbResNo));
}
@Test(groups = { "Functional" })
git://source.jalview.org / jalview.git / commitdiff