import java.io.IOException;
import java.net.URL;
import java.util.ArrayList;
-import java.util.Hashtable;
import java.util.List;
import java.util.StringTokenizer;
import java.util.Vector;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.AlignViewport;
-import jalview.gui.AlignmentPanel;
import jalview.gui.CalculationChooser;
import jalview.gui.Desktop;
import jalview.gui.StructureViewer;
import jalview.io.JPredFile;
import jalview.io.JnetAnnotationMaker;
import jalview.io.NewickFile;
-import jalview.renderer.seqfeatures.FeatureRenderer;
import jalview.structure.SelectionListener;
import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
// be '|', but many sequence IDS include
// pipes.
+ /**
+ * We maintain a pointer to the jalview instance here, because only with that do we have a direct
+ * connection from the JavaScript "applet" object to the proper instance of Jalview in case there
+ * are multiple applets on a page.
+ */
+ private Jalview jalview;
+
- public JalviewJSApp(ArgsParser aparser)
+ public JalviewJSApp(Jalview jalview, ArgsParser aparser)
{
+ this.jalview = jalview;
this.aparser = aparser;
Platform.setAppClass(this);
}
// private boolean alignPDBStructures; // From JalviewLite; not implemented
//
- private Hashtable<String, Hashtable<String, String[]>> jsmessages;
-
- private Hashtable<String, int[]> jshashes;
-
+
@Override
public String getParameter(String name)
{
}
@Override
- public Hashtable<String, int[]> getJSHashes()
- {
- return (jshashes == null ? (jshashes = new Hashtable<>()) : jshashes);
- }
-
- @Override
- public Hashtable<String, Hashtable<String, String[]>> getJSMessages()
- {
- return (jsmessages == null ? (jsmessages = new Hashtable<>())
- : jsmessages);
- }
-
- @Override
- public Object getJSObject()
- {
- return Jalview.getInstance();
- }
-
- @Override
- public FeatureRenderer getNewFeatureRenderer(AlignViewportI vp)
- {
- return new jalview.gui.FeatureRenderer((AlignmentPanel) vp);
- }
-
- @Override
public Object[] getSelectionForListener(SequenceGroup seqsel,
ColumnSelection colsel, HiddenColumns hidden,
SelectionSource source, Object alignFrame)
}
+ /**
+ * @j2sAlias showStructure
+ */
+ @Override
+ public void showStructure(AlignFrame af, String pdbID, String fileType) {
+ if (af == null)
+ af = Jalview.getCurrentAlignFrame();
+ PDBEntry pe = null;
+ SequenceI[] seqs = null;
+ if (pdbID == null) {
+ seqs = af.getViewport().getSequenceSelection();
+ if (seqs.length == 0)
+ seqs = af.getViewport().getAlignment().getSequencesArray();
+ for (int i = 0; i < seqs.length; i++) {
+ Vector<PDBEntry> list = seqs[i].getAllPDBEntries();
+ if (list.size() > 0) {
+ pe = list.get(0);
+ break;
+ }
+ }
+ }
+ if (pe == null) {
+ if (pdbID == null)
+ return;
+ pe = new PDBEntry(pdbID, null, fileType);
+ List<SequenceI> list = af.getViewport().getAlignment().getSequences();
+ List<SequenceI> tmp = new ArrayList<SequenceI>();
+ for (int i = 0; i < list.size(); i++) {
+ SequenceI seq = list.get(i);
+ if (seq.getPDBEntry(pdbID) != null) {
+ tmp.add(seq);
+ }
+ }
+ seqs = tmp.toArray(new SequenceI[tmp.size()]);
+ af.alignPanel.selectSequences(tmp);
+ }
+ StructureViewer.launchStructureViewer(
+ af.alignPanel,
+ pe, seqs);
+ }
+
public void newStructureView(AlignFrame af, PDBEntry pdb,
SequenceI[] seqs, String[] chains, DataSourceType protocol)
{
return parseFeaturesFile(null, filename, protocol);
}
+ /**
+ * @j2sAlias parseFeatureFile
+ *
+ * @param af
+ * @param filename
+ * @param protocol
+ * @return
+ */
public boolean parseFeaturesFile(AlignFrame af, String filename, DataSourceType protocol)
{
- return af.parseFeaturesFile(filename, protocol);
- }
-
- @Override
- public void setFeatureGroupState(String[] groups, boolean state)
- {
- setFeatureGroupState(null, groups, state);
+ return (af == null ? Jalview.getCurrentAlignFrame() : af).parseFeaturesFile(filename, protocol);
}
- public void setFeatureGroupState(AlignFrame af, String[] groups, boolean state) {
- (af == null ? Jalview.getCurrentAlignFrame() : af).setFeatureGroupState(groups, state);
- }
/**
* annotations, jpredfile, jnetfile
*
}
@Override
- public boolean addPdbFile(AlignFrame alf, String sequenceId,
- String pdbEntryString, String pdbFile)
+ public boolean addPdbFile(AlignFrame alf, String sequenceId, String pdbId,
+ String pdbFile)
{
if (alf == null)
{
alf = Jalview.getCurrentAlignFrame();
}
- SequenceI toaddpdb = alf.getViewport().getAlignment()
- .findName(sequenceId);
- boolean needtoadd = false;
- if (toaddpdb != null)
+ SequenceI seq = alf.getViewport().getAlignment().findName(sequenceId);
+ if (seq != null)
{
- Vector<PDBEntry> pdbe = toaddpdb.getAllPDBEntries();
+ Vector<PDBEntry> pdbe = seq.getAllPDBEntries();
PDBEntry pdbentry = null;
if (pdbe != null && pdbe.size() > 0)
{
for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
{
pdbentry = pdbe.elementAt(pe);
- if (!pdbentry.getId().equals(pdbEntryString)
- && !pdbentry.getFile().equals(pdbFile))
+ if (!pdbentry.getId().equals(pdbId)
+ || pdbFile != null && !pdbentry.getFile().equals(pdbFile))
{
pdbentry = null;
}
- else
- {
- continue;
- }
}
}
if (pdbentry == null)
{
- pdbentry = new PDBEntry();
- pdbentry.setId(pdbEntryString);
- pdbentry.setFile(pdbFile);
- needtoadd = true; // add this new entry to sequence.
- }
- // resolve data source
- // TODO: this code should be a refactored to an io package
- DataSourceType protocol = AppletFormatAdapter.resolveProtocol(pdbFile,
- FileFormat.PDB);
- if (protocol == null)
- {
- return false;
- }
- if (needtoadd)
- {
- pdbentry.setProperty("protocol", protocol);
- toaddpdb.addPDBId(pdbentry);
+ pdbentry = new PDBEntry(pdbId, null, pdbFile);
+ if (pdbFile != null)
+ {
+ DataSourceType protocol = AppletFormatAdapter
+ .resolveProtocol(pdbFile, FileFormat.PDB);
+ if (protocol == null)
+ return false;
+ pdbentry.setProperty("protocol", protocol);
+ }
+ seq.addPDBId(pdbentry);
alf.alignPanel.getStructureSelectionManager()
.registerPDBEntry(pdbentry);
}
return true;
}
- @Override
- public String arrayToSeparatorList(String[] array)
- {
- return arrayToSeparatorList(array, separator);
- }
-
- /**
- * concatenate the list with separator
- *
- * @param list
- * @param separator
- * @return concatenated string
- */
- public static String arrayToSeparatorList(String[] list, String separator)
- {
- // TODO use StringUtils version
- StringBuffer v = new StringBuffer();
- if (list != null && list.length > 0)
- {
- for (int i = 0, iSize = list.length; i < iSize; i++)
- {
- if (list[i] != null)
- {
- if (i > 0)
- {
- v.append(separator);
- }
- v.append(list[i]);
- }
- }
- // if (debug)
- // {
- // System.err
- // .println("Returning '" + separator + "' separated List:\n");
- // System.err.println(v);
- // }
- return v.toString();
- }
- // if (debug)
- // {
- // System.err.println(
- // "Returning empty '" + separator + "' separated List\n");
- // }
- return "" + separator;
- }
+// @Override
+// public String arrayToSeparatorList(String[] array)
+// {
+// return arrayToSeparatorList(array, separator);
+// }
+
+// /**
+// * concatenate the list with separator
+// *
+// * @param list
+// * @param separator
+// * @return concatenated string
+// */
+// public static String arrayToSeparatorList(String[] list, String separator)
+// {
+// // TODO use StringUtils version
+// StringBuffer v = new StringBuffer();
+// if (list != null && list.length > 0)
+// {
+// for (int i = 0, iSize = list.length; i < iSize; i++)
+// {
+// if (list[i] != null)
+// {
+// if (i > 0)
+// {
+// v.append(separator);
+// }
+// v.append(list[i]);
+// }
+// }
+// // if (debug)
+// // {
+// // System.err
+// // .println("Returning '" + separator + "' separated List:\n");
+// // System.err.println(v);
+// // }
+// return v.toString();
+// }
+// // if (debug)
+// // {
+// // System.err.println(
+// // "Returning empty '" + separator + "' separated List\n");
+// // }
+// return "" + separator;
+// }
@Override
public String getAlignment(String format)
return getAlignmentFrom(null, format, null);
}
+ /**
+ * suffix string "true"/"false" (default true)
+ * passed to AlnFile class controls whether /START-END is added to
+ * sequence names
+ */
@Override
public String getAlignment(String format, String suffix)
{
}
@Override
- public String getAlignmentOrderFrom(AlignFrame alf)
- {
- return getAlignmentFrom(alf, null);
- }
-
- @Override
- public String getAlignmentOrderFrom(AlignFrame alf, String sep)
+ public String[] getAlignmentOrderFrom(AlignFrame alf)
{
if (alf == null)
{
{
order[i] = alorder.getSequenceAt(i).getName();
}
- return arrayToSeparatorList(order, sep);
+ return order;// arrayToSeparatorList(order, sep);
}
@Override
}
@Override
- public String getFeatureGroups()
+ public String[] getFeatureGroups()
{
return getFeatureGroupsOn(null);
}
@Override
- public String getFeatureGroupsOfState(boolean visible)
+ public String[] getFeatureGroupsOfState(boolean visible)
{
return getFeatureGroupsOfStateOn(null, visible);
}
@Override
- public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
+ public String[] getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
{
if (alf == null)
{
alf = Jalview.getCurrentAlignFrame();
}
- return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));
+ return alf.getFeatureGroupsOfState(visible);
}
@Override
- public String getFeatureGroupsOn(AlignFrame alf)
+ public String[] getFeatureGroupsOn(AlignFrame alf)
{
if (alf == null)
{
alf = Jalview.getCurrentAlignFrame();
}
- return arrayToSeparatorList(alf.getFeatureGroups());
+ return alf.getFeatureGroups();
}
@Override
return features;
}
-
- @Override
- public String getJsMessage(String messageclass, String viewId)
- {
- // TODO Auto-generated method stub
- return null;
- }
-
+
/**
* read sequence1...sequenceN as a raw alignment
*
* @see jalview.appletgui.js.JalviewLiteJsApi#getSelectedSequences()
*/
@Override
- public String getSelectedSequences()
+ public SequenceI[] getSelectedSequences()
{
return getSelectedSequencesFrom(Jalview.getCurrentAlignFrame());
}
* @see jalview.appletgui.js.JalviewLiteJsApi#getSelectedSequences(java.lang.String)
*/
@Override
- public String getSelectedSequences(String sep)
+ public SequenceI[] getSelectedSequences(String sep)
{
return getSelectedSequencesFrom(Jalview.getCurrentAlignFrame(), sep);
}
* .AlignFrame)
*/
@Override
- public String getSelectedSequencesFrom(AlignFrame alf)
+ public SequenceI[] getSelectedSequencesFrom(AlignFrame alf)
{
return getSelectedSequencesFrom(alf, null);
}
@Override
- public String getSelectedSequencesFrom(AlignFrame alf, String sep)
+ public SequenceI[] getSelectedSequencesFrom(AlignFrame alf, String sep)
{
if (alf == null)
{
alf = Jalview.getCurrentAlignFrame();
}
- StringBuffer result = new StringBuffer("");
- if (sep == null || sep.length() == 0)
- {
- sep = separator; // "+0x00AC;
- }
AlignViewport v = alf.getViewport();
if (v.getSelectionGroup() != null)
{
- SequenceI[] seqs = v.getSelectionGroup()
+ return v.getSelectionGroup()
.getSequencesInOrder(v.getAlignment());
-
- for (int i = 0; i < seqs.length; i++)
- {
- result.append(seqs[i].getName());
- result.append(sep);
- }
}
- return result.toString();
+ return null;
}
public Object[] getSelectionForListener(AlignFrame alf,
cols[0] = "" + (1 + strt) + "-" + (1 + end);
}
}
- return new Object[] { src, setid, arrayToSeparatorList(seqs),
- arrayToSeparatorList(cols) };
- }
-
- @Override
- public String getSeparator()
- {
- return separator;
+ return new Object[] { src, setid, seqs, cols };
}
/**
}
/**
+ * @j2sAlias openPcaPanel
+ *
* public static method for JalviewJS API to open a PCAPanel without
* necessarily using a dialog.
*
}
/**
+ * @j2sAlias openTreePanel
+ *
* Open a new Tree panel on the desktop statically. Params are standard (not
* set by Groovy). No dialog is opened.
*
return CalculationChooser.openTreePanel(af, treeType, modelName, null);
}
+
@Override
- public String orderAlignmentBy(AlignFrame alf, String order,
- String undoName, String sep)
+ public String orderBy(String[] ids, String undoName)
{
- if (sep == null || sep.length() == 0)
- {
- sep = separator;
- }
- String[] ids = separatorListToArray(order, sep);
+ return orderAlignmentBy(null, ids, undoName);
+ }
+
+ @Override
+ public String orderAlignmentBy(AlignFrame alf, String[] ids,
+ String undoName)
+ {
+ if (alf == null)
+ alf = Jalview.getCurrentAlignFrame();
SequenceI[] sqs = null;
if (ids != null && ids.length > 0)
{
- if (alf == null)
- {
- alf = Jalview.getCurrentAlignFrame();
- }
jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
alf.getViewport().getAlignment().getSequencesArray());
int s = 0;
return alf.sortBy(aorder, _undoName) ? "true" : "";
}
- @Override
- public String orderBy(String order, String undoName)
- {
- return orderBy(order, undoName, null);
- }
-
- @Override
- public String orderBy(String order, String undoName, String sep)
- {
- return orderAlignmentBy(Jalview.getCurrentAlignFrame(), order, undoName,
- sep);
- }
-
/**
* Allow an outside entity to initiate the second half of argument parsing
* (only).
try
{
- Jalview.getInstance().parseArguments(new ArgsParser(args), false);
+ jalview.parseArguments(new ArgsParser(args), false);
return null;
} catch (Throwable t)
{
}
}
- // public AlignFrame newViewFrom(AlignFrame alf, String name)
- // {
- // return (AlignFrame) alf.newView(name, true);
- // }
- //
@Override
- public String[] separatorListToArray(String list)
+ public void setFeatureGroupState(String[] groups, boolean state)
{
- return separatorListToArray(list, separator);
+ setFeatureGroupState(null, groups, state);
}
@Override
public void setFeatureGroupStateOn(final AlignFrame alf,
final String groups, boolean state)
{
+ setFeatureGroupState(alf, separatorListToArray(groups, separator), state);
+// java.awt.EventQueue.invokeLater(new Runnable()
+// {
+// @Override
+// public void run()
+// {
+// (alf == null ? Jalview.getCurrentAlignFrame() : alf)
+// .setFeatureGroupState(
+// separatorListToArray(groups, separator), state);
+// }
+// });
+ }
- java.awt.EventQueue.invokeLater(new Runnable()
- {
- @Override
- public void run()
- {
- (alf == null ? Jalview.getCurrentAlignFrame() : alf)
- .setFeatureGroupState(
- separatorListToArray(groups, separator), state);
- }
- });
+ public void setFeatureGroupState(AlignFrame af, String[] groups, boolean state) {
+ (af == null ? Jalview.getCurrentAlignFrame() : af).setFeatureGroupState(groups, state);
}
+
@Override
public void setSelectionListener(AlignFrame af, String listener)
{
}
@Override
- public void setSeparator(String separator)
- {
- this.separator = separator;
- }
-
- @Override
public void showOverview()
{
Jalview.getCurrentAlignFrame().overviewMenuItem_actionPerformed(null);
*/
public String doSendCallback(Object callback, Object[] data)
{
- Jalview me = Jalview.getInstance();
+ Jalview me = jalview;
if (me != null && callback != null)
{
if (seqsel != null && seqsel.getSize() > 0)
{
// send a valid range, otherwise we send the empty selection
- cols = new String[2];
+ cols = new String[1];
cols[0] = "" + (1 + strt) + "-" + (1 + end);
}
;
doSendCallback(_listener,
new Object[]
- { src, setid, arrayToSeparatorList(seqs),
- arrayToSeparatorList(cols) });
+ { src, setid, seqs, cols });
}
public boolean isFor(AlignFrame af, String listener)
git://source.jalview.org / jalview.git / blobdiff