/*
- * 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 java.applet.*;
-
-import java.awt.*;
-import java.awt.event.*;
+import jalview.appletgui.AlignFrame;
+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.Color;
+import java.awt.Component;
+import java.awt.Font;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.event.ActionEvent;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
import java.io.BufferedReader;
import java.io.InputStreamReader;
-import java.util.*;
-
-import jalview.appletgui.*;
-import jalview.datamodel.*;
-import jalview.io.*;
+import java.util.StringTokenizer;
+import java.util.Vector;
/**
* Jalview Applet. Runs in Java 1.18 runtime
}
/**
+ *
+ * @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);
+ }
+
// //////////////////////////////////////////////
// //////////////////////////////////////////////
- static int lastFrameX = 200;
+ public static int lastFrameX = 200;
- static int lastFrameY = 200;
+ public static int lastFrameY = 200;
boolean fileFound = true;
public boolean jmolAvailable = false;
+ private boolean alignPdbStructures = false;
+
public static boolean debug = false;
static String builddate = null, version = null;
*/
public void init()
{
-
+ // remove any handlers that might be hanging around from an earlier instance
+
/**
* turn on extra applet debugging
*/
ex.printStackTrace();
}
}
-
+ /*
+ * <param name="alignpdbfiles" value="false/true"/> Undocumented for 2.6
+ * - related to JAL-434
+ */
+ applet.setAlignPdbStructures(getDefaultParameter("alignpdbfiles",
+ false));
/*
* <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B
* PDB|1GAQ|1GAQ|C">
*/
int pdbFileCount = 0;
+ // Accumulate pdbs here if they are heading for the same view (if
+ // alignPdbStructures is true)
+ Vector pdbs = new Vector();
do
{
if (pdbFileCount > 0)
// the local pdb file was identified in the class loader
protocol = AppletFormatAdapter.URL; // this is probably NOT
// CORRECT!
- param = addProtocol(param); //
+ param = addProtocol(param); //
}
pdb.setFile(param);
}
}
- if (jmolAvailable)
+ if (!alignPdbStructures)
{
- new jalview.appletgui.AppletJmol(pdb, seqs, chains,
- newAlignFrame.alignPanel, protocol);
- lastFrameX += 40;
- lastFrameY += 40;
+ newAlignFrame.newStructureView(applet, pdb, seqs, chains,
+ protocol);
}
else
- new MCview.AppletPDBViewer(pdb, seqs, chains,
- newAlignFrame.alignPanel, protocol);
+ {
+ pdbs.addElement(new Object[]
+ { pdb, seqs, chains, new String(protocol) });
+ }
}
}
pdbFileCount++;
} while (pdbFileCount < 10);
+ 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++)
+ {
+ Object[] o = (Object[]) pdbs.elementAt(pdbsi);
+ pdb[pdbsi] = (PDBEntry) o[0];
+ seqs[pdbsi] = (SequenceI[]) o[1];
+ chains[pdbsi] = (String[]) o[2];
+ protocols[pdbsi] = (String) o[3];
+ }
+ 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;
}
/**
}
return false;
}
+
+ /**
+ * bind a pdb file to a sequence in the given alignFrame.
+ *
+ * @param alFrame
+ * - null or specific alignFrame. This specifies the dataset that
+ * will be searched for a seuqence called sequenceId
+ * @param sequenceId
+ * - sequenceId within the dataset.
+ * @param pdbEntryString
+ * - the short name for the PDB file
+ * @param pdbFile
+ * - pdb file - either a URL or a valid PDB file.
+ * @return true if binding was as success TODO: consider making an exception
+ * structure for indicating when PDB parsing or seqeunceId location
+ * fails.
+ */
+ public boolean addPdbFile(AlignFrame alFrame, String sequenceId,
+ String pdbEntryString, String pdbFile)
+ {
+ return alFrame.addPdbFile(sequenceId, pdbEntryString, pdbFile);
+ }
+
+ protected void setAlignPdbStructures(boolean alignPdbStructures)
+ {
+ this.alignPdbStructures = alignPdbStructures;
+ }
+
+ public boolean isAlignPdbStructures()
+ {
+ return alignPdbStructures;
+ }
+
+ /**
+ * get all components associated with the applet of the given type
+ *
+ * @param class1
+ * @return
+ */
+ public Vector getAppletWindow(Class class1)
+ {
+ Vector wnds = new Vector();
+ Component[] cmp = getComponents();
+ if (cmp != null)
+ {
+ for (int i = 0; i < cmp.length; i++)
+ {
+ 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 alFrame
+ * @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; }
+ */
}
git://source.jalview.org / jalview.git / blobdiff