/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*/
package jalview.bin;
-import jalview.api.SequenceStructureBinding;
import jalview.appletgui.AlignFrame;
-import jalview.appletgui.AppletJmol;
import jalview.appletgui.EmbmenuFrame;
import jalview.appletgui.FeatureSettings;
import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.io.AnnotationFile;
import jalview.io.AppletFormatAdapter;
import jalview.io.FileParse;
import jalview.io.IdentifyFile;
import jalview.io.JnetAnnotationMaker;
+import jalview.javascript.JsCallBack;
+import jalview.structure.SelectionListener;
+import jalview.structure.StructureSelectionManager;
import java.applet.Applet;
import java.awt.Button;
import java.awt.event.WindowEvent;
import java.io.BufferedReader;
import java.io.InputStreamReader;
-import java.lang.reflect.Method;
-import java.util.Enumeration;
import java.util.StringTokenizer;
import java.util.Vector;
}
/**
+ *
+ * @param sequenceId id of sequence to highlight
+ * @param position integer position [ tobe implemented or range ] on sequence
+ * @param alignedPosition true/false/empty string - indicate if position is an alignment column or unaligned sequence position
+ */
+ public void highlight(String sequenceId, String position, String alignedPosition)
+ {
+ highlight(currentAlignFrame, sequenceId, position, alignedPosition);
+ }
+ /**
+ *
+ * @param sequenceId id of sequence to highlight
+ * @param position integer position [ tobe implemented or range ] on sequence
+ * @param alignedPosition false, blank or something else - indicate if position is an alignment column or unaligned sequence position
+ */
+ public void highlight(AlignFrame alf, String sequenceId, String position, String alignedPosition)
+ {
+ SequenceI sq = alf.getAlignViewport().getAlignment().findName(sequenceId);
+ if (sq!=null)
+ {
+ int pos, apos=-1;
+ try {
+ apos = new Integer(position).intValue();
+ apos--;
+ } catch (NumberFormatException ex)
+ {
+ return;
+ }
+ // use vamsas listener to broadcast to all listeners in scope
+ if (alignedPosition!=null && (alignedPosition.trim().length()==0 || alignedPosition.toLowerCase().indexOf("false")>-1))
+ {
+ StructureSelectionManager.getStructureSelectionManager().mouseOverVamsasSequence(sq,sq.findIndex(apos));
+ } else {
+ StructureSelectionManager.getStructureSelectionManager().mouseOverVamsasSequence(sq,apos);
+ }
+
+ }
+ }
+ /**
+ * select regions of the currrent alignment frame
+ *
+ * @param sequenceIds String separated list of sequence ids or empty string
+ * @param columns
+ * String separated list { column range or column, ..} or empty string
+ */
+ public void select(String sequenceIds, String columns)
+ {
+ select(currentAlignFrame, sequenceIds, columns, "¬");
+ }
+
+ /**
+ * select regions of the currrent alignment frame
+ *
+ * @param toselect
+ * String separated list { column range, seq1...seqn sequence ids }
+ * @param sep
+ * separator between toselect fields
+ */
+ public void select(String sequenceIds, String columns, String sep)
+ {
+ select(currentAlignFrame, sequenceIds, columns, sep);
+ }
+
+ /**
+ * select regions of the given alignment frame
+ *
+ * @param alf
+ * @param toselect
+ * String separated list { column range, seq1...seqn sequence ids }
+ * @param sep
+ * separator between toselect fields
+ */
+ public void select(AlignFrame alf, String sequenceIds, String columns)
+ {
+ select(alf, sequenceIds, columns, separator);
+ }
+
+ /**
+ * select regions of the given alignment frame
+ *
+ * @param alf
+ * @param toselect
+ * String separated list { column range, seq1...seqn sequence ids }
+ * @param sep
+ * separator between toselect fields
+ */
+ public void select(AlignFrame alf, String sequenceIds, String columns,
+ String sep)
+ {
+ if (sep == null || sep.length() == 0)
+ {
+ sep = separator;
+ }
+ // deparse fields
+ String[] ids = separatorListToArray(sequenceIds, sep);
+ String[] cols = separatorListToArray(columns, sep);
+ SequenceGroup sel = new SequenceGroup();
+ ColumnSelection csel = new ColumnSelection();
+ AlignmentI al = alf.viewport.getAlignment();
+ int start = 0, end = al.getWidth(), alw = al.getWidth();
+ if (ids != null && ids.length > 0)
+ {
+ for (int i = 0; i < ids.length; i++)
+ {
+ if (ids[i].trim().length() == 0)
+ {
+ continue;
+ }
+ SequenceI sq = al.findName(ids[i]);
+ if (sq != null)
+ {
+ sel.addSequence(sq, false);
+ }
+ }
+ }
+ if (cols != null && cols.length > 0)
+ {
+ boolean seset = false;
+ for (int i = 0; i < cols.length; i++)
+ {
+ String cl = cols[i].trim();
+ if (cl.length() == 0)
+ {
+ continue;
+ }
+ int p;
+ if ((p = cl.indexOf("-")) > -1)
+ {
+ int from = -1, to = -1;
+ try
+ {
+ from = new Integer(cl.substring(0, p)).intValue();
+ from--;
+ } catch (NumberFormatException ex)
+ {
+ System.err
+ .println("ERROR: Couldn't parse first integer in range element column selection string '"
+ + cl + "' - format is 'from-to'");
+ return;
+ }
+ try
+ {
+ to = new Integer(cl.substring(p + 1)).intValue();
+ to--;
+ } catch (NumberFormatException ex)
+ {
+ System.err
+ .println("ERROR: Couldn't parse second integer in range element column selection string '"
+ + cl + "' - format is 'from-to'");
+ return;
+ }
+ if (from >= 0 && to >= 0)
+ {
+ // valid range
+ if (from < to)
+ {
+ int t = to;
+ to = from;
+ to = t;
+ }
+ if (!seset)
+ {
+ start = from;
+ end = to;
+ seset = true;
+ }
+ else
+ {
+ // comment to prevent range extension
+ if (start > from)
+ {
+ start = from;
+ }
+ if (end < to)
+ {
+ end = to;
+ }
+ }
+ for (int r = from; r <= to; r++)
+ {
+ if (r >= 0 && r < alw)
+ {
+ csel.addElement(r);
+ }
+ }
+ if (debug)
+ {
+ System.err.println("Range '" + cl + "' deparsed as [" + from
+ + "," + to + "]");
+ }
+ }
+ else
+ {
+ System.err.println("ERROR: Invalid Range '" + cl
+ + "' deparsed as [" + from + "," + to + "]");
+ }
+ }
+ else
+ {
+ int r = -1;
+ try
+ {
+ r = new Integer(cl).intValue();
+ r--;
+ } catch (NumberFormatException ex)
+ {
+ System.err
+ .println("ERROR: Couldn't parse integer from point selection element of column selection string '"
+ + cl + "'");
+ return;
+ }
+ if (r >= 0 && r <= alw)
+ {
+ if (!seset)
+ {
+ start = r;
+ end = r;
+ seset = true;
+ }
+ else
+ {
+ // comment to prevent range extension
+ if (start > r)
+ {
+ start = r;
+ }
+ if (end < r)
+ {
+ end = r;
+ }
+ }
+ csel.addElement(r);
+ if (debug)
+ {
+ System.err.println("Point selection '" + cl
+ + "' deparsed as [" + r + "]");
+ }
+ }
+ else
+ {
+ System.err.println("ERROR: Invalid Point selection '" + cl
+ + "' deparsed as [" + r + "]");
+ }
+ }
+ }
+ }
+ sel.setStartRes(start);
+ sel.setEndRes(end);
+ alf.select(sel, csel);
+
+ }
+
+ /**
* get sequences selected in current alignFrame and return their alignment in
* format 'format' either with or without suffix
*
return null;
}
+ public void setMouseoverListener(String listener)
+ {
+ setMouseoverListener(currentAlignFrame, listener);
+ }
+
+ private Vector mouseoverListeners = new Vector();
+
+ public void setMouseoverListener(AlignFrame af, String listener)
+ {
+ if (listener != null)
+ {
+ listener = listener.trim();
+ if (listener.length() == 0)
+ {
+ System.err
+ .println("jalview Javascript error: Ignoring empty function for mouseover listener.");
+ return;
+ }
+ }
+ jalview.javascript.MouseOverListener mol = new jalview.javascript.MouseOverListener(
+ this, af, listener);
+ mouseoverListeners.addElement(mol);
+ StructureSelectionManager.getStructureSelectionManager()
+ .addStructureViewerListener(mol);
+ if (debug)
+ {
+ System.err.println("Added a mouseover listener for "
+ + ((af == null) ? "All frames" : "Just views for "
+ + af.getAlignViewport().getSequenceSetId()));
+ System.err.println("There are now " + mouseoverListeners.size()
+ + " listeners in total.");
+ }
+ }
+
+ public void setSelectionListener(String listener)
+ {
+ setSelectionListener(null, listener);
+ }
+
+ public void setSelectionListener(AlignFrame af, String listener)
+ {
+ if (listener != null)
+ {
+ listener = listener.trim();
+ if (listener.length() == 0)
+ {
+ System.err
+ .println("jalview Javascript error: Ignoring empty function for selection listener.");
+ return;
+ }
+ }
+ jalview.javascript.JsSelectionSender mol = new jalview.javascript.JsSelectionSender(
+ this, af, listener);
+ mouseoverListeners.addElement(mol);
+ StructureSelectionManager.getStructureSelectionManager()
+ .addSelectionListener(mol);
+ if (debug)
+ {
+ System.err.println("Added a selection listener for "
+ + ((af == null) ? "All frames" : "Just views for "
+ + af.getAlignViewport().getSequenceSetId()));
+ System.err.println("There are now " + mouseoverListeners.size()
+ + " listeners in total.");
+ }
+ }
+
+ /**
+ * remove any callback using the given listener function and associated with
+ * the given alignFrame (or null for all callbacks)
+ *
+ * @param af
+ * (may be null)
+ * @param listener
+ * (may be null)
+ */
+ public void removeJavascriptListener(AlignFrame af, String listener)
+ {
+ if (listener != null)
+ {
+ listener = listener.trim();
+ if (listener.length() == 0)
+ {
+ listener = null;
+ }
+ }
+ boolean rprt = false;
+ for (int ms=0,msSize=mouseoverListeners.size();ms<msSize;)
+ {
+ Object lstn = mouseoverListeners.elementAt(ms);
+ JsCallBack lstner = (JsCallBack) lstn;
+ if ((af == null || lstner.getAlignFrame() == af)
+ && (listener == null || lstner.getListenerFunction().equals(
+ listener)))
+ {
+ mouseoverListeners.removeElement(lstner);
+ msSize--;
+ if (lstner instanceof SelectionListener)
+ {
+ StructureSelectionManager.getStructureSelectionManager()
+ .removeSelectionListener((SelectionListener) lstner);
+ }
+ else
+ {
+ StructureSelectionManager.getStructureSelectionManager()
+ .removeStructureViewerListener(lstner, null);
+ }
+ rprt = debug;
+ if (debug)
+ {
+ System.err.println("Removed listener '" + listener + "'");
+ }
+ } else {
+ ms++;
+ }
+ }
+ if (rprt)
+ {
+ System.err.println("There are now " + mouseoverListeners.size()
+ + " listeners in total.");
+ }
+ }
+
+ public void stop()
+ {
+ if (mouseoverListeners!=null)
+ {
+ while (mouseoverListeners.size()>0)
+ {
+ Object mol = mouseoverListeners.elementAt(0);
+ mouseoverListeners.removeElement(mol);
+ if (mol instanceof SelectionListener)
+ {
+ StructureSelectionManager.getStructureSelectionManager().removeSelectionListener((SelectionListener)mol);
+ } else {
+ StructureSelectionManager.getStructureSelectionManager().removeStructureViewerListener(mol, null);
+ }
+ }
+ }
+ }
+ /**
+ * send a mouseover message to all the alignment windows associated with the
+ * given residue in the pdbfile
+ *
+ * @param pdbResNum
+ * @param chain
+ * @param pdbfile
+ */
+ public void mouseOverStructure(int pdbResNum, String chain, String pdbfile)
+ {
+ StructureSelectionManager.getStructureSelectionManager()
+ .mouseOverStructure(pdbResNum, chain, pdbfile);
+ }
+
// //////////////////////////////////////////////
// //////////////////////////////////////////////
public boolean jmolAvailable = false;
- private boolean alignPdbStructures=false;
+ private boolean alignPdbStructures = false;
public static boolean debug = false;
*/
public void init()
{
-
+ // remove any handlers that might be hanging around from an earlier instance
+
/**
* turn on extra applet debugging
*/
}
}
/*
- * <param name="alignpdbfiles" value="false/true"/>
- * Undocumented for 2.6 - related to JAL-434
+ * <param name="alignpdbfiles" value="false/true"/> Undocumented for 2.6
+ * - related to JAL-434
*/
- applet.setAlignPdbStructures(getDefaultParameter("alignpdbfiles",false));
+ applet.setAlignPdbStructures(getDefaultParameter("alignpdbfiles",
+ false));
/*
* <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B
* PDB|1GAQ|1GAQ|C">
*
* <param name="PDBfile3" value="1q0o Q45135_9MICO">
*/
-
+
int pdbFileCount = 0;
- // Accumulate pdbs here if they are heading for the same view (if alignPdbStructures is true)
- Vector pdbs=new Vector();
+ // Accumulate pdbs here if they are heading for the same view (if
+ // alignPdbStructures is true)
+ Vector pdbs = new Vector();
do
{
if (pdbFileCount > 0)
}
}
}
-
- if (!alignPdbStructures) {
+
+ if (!alignPdbStructures)
+ {
newAlignFrame.newStructureView(applet, pdb, seqs, chains,
- protocol);
- } else {
- pdbs.addElement(new Object[] { pdb, seqs, chains, new String(protocol)});
+ protocol);
+ }
+ else
+ {
+ pdbs.addElement(new Object[]
+ { pdb, seqs, chains, new String(protocol) });
}
}
}
pdbFileCount++;
} while (pdbFileCount < 10);
- if (pdbs.size()>0)
+ if (pdbs.size() > 0)
{
SequenceI[][] seqs = new SequenceI[pdbs.size()][];
PDBEntry[] pdb = new PDBEntry[pdbs.size()];
String[][] chains = new String[pdbs.size()][];
String[] protocols = new String[pdbs.size()];
- for (int pdbsi=0,pdbsiSize=pdbs.size(); pdbsi<pdbsiSize;pdbsi++)
+ for (int pdbsi = 0, pdbsiSize = pdbs.size(); pdbsi < pdbsiSize; pdbsi++)
{
Object[] o = (Object[]) pdbs.elementAt(pdbsi);
pdb[pdbsi] = (PDBEntry) o[0];
chains[pdbsi] = (String[]) o[2];
protocols[pdbsi] = (String) o[3];
}
- newAlignFrame.alignedStructureView(applet, pdb, seqs, chains, protocols);
-
+ newAlignFrame.alignedStructureView(applet, pdb, seqs, chains,
+ protocols);
+
}
// ///////////////////////////
// modify display of features
*/
public String[] separatorListToArray(String list)
{
+ return separatorListToArray(list, separator);
+ }
+
+ /**
+ * parse the string into a list
+ *
+ * @param list
+ * @param separator
+ * @return elements separated by separator
+ */
+ public String[] separatorListToArray(String list, String separator)
+ {
+ // note separator local variable intentionally masks object field
int seplen = separator.length();
- if (list == null || list.equals(""))
+ if (list == null || list.equals("") || list.equals(separator))
return null;
java.util.Vector jv = new Vector();
int cp = 0, pos;
*/
public String arrayToSeparatorList(String[] list)
{
+ return arrayToSeparatorList(list, separator);
+ }
+
+ /**
+ * concatenate the list with separator
+ *
+ * @param list
+ * @param separator
+ * @return concatenated string
+ */
+ public String arrayToSeparatorList(String[] list, String separator)
+ {
StringBuffer v = new StringBuffer();
- if (list != null)
+ if (list != null && list.length > 0)
{
for (int i = 0, iSize = list.length - 1; i < iSize; i++)
{
System.err.println("Returning empty '" + separator
+ "' separated List\n");
}
- return "";
+ return "" + separator;
}
/**
}
/**
- * get all components associated with the applet of the given type
+ * get all components associated with the applet of the given type
+ *
* @param class1
* @return
*/
{
Vector wnds = new Vector();
Component[] cmp = getComponents();
- if (cmp!=null)
+ if (cmp != null)
{
- for (int i=0;i<cmp.length;i++)
- {
- if (class1.isAssignableFrom(cmp[i].getClass()))
+ for (int i = 0; i < cmp.length; i++)
{
- wnds.addElement(cmp);
+ if (class1.isAssignableFrom(cmp[i].getClass()))
+ {
+ wnds.addElement(cmp);
+ }
}
- }}
+ }
return wnds;
}
-
/**
* bind structures in a viewer to any matching sequences in an alignFrame (use
* sequenceIds to limit scope of search to specific sequences)
* @param viewer
* @param sequenceIds
* @return TODO: consider making an exception structure for indicating when
- * binding fails
- public SequenceStructureBinding addStructureViewInstance(
- AlignFrame alFrame, Object viewer, String sequenceIds)
- {
-
- if (sequenceIds != null && sequenceIds.length() > 0)
- {
- return alFrame.addStructureViewInstance(viewer,
- separatorListToArray(sequenceIds));
- }
- else
- {
- return alFrame.addStructureViewInstance(viewer, null);
- }
- // return null;
- }
+ * binding fails public SequenceStructureBinding
+ * addStructureViewInstance( AlignFrame alFrame, Object viewer, String
+ * sequenceIds) {
+ *
+ * if (sequenceIds != null && sequenceIds.length() > 0) { return
+ * alFrame.addStructureViewInstance(viewer,
+ * separatorListToArray(sequenceIds)); } else { return
+ * alFrame.addStructureViewInstance(viewer, null); } // return null; }
*/
}
git://source.jalview.org / jalview.git / blobdiff