X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=1801eb1cd38de7a0d5208033e522f8b1a0c41b5c;hb=af1471fa3d7d3cb32d203e81d394838608dd1c96;hp=0e77f021a28b3f0e6b1cc13ae05b6ce00a97af09;hpb=e1a2bb8c2129346c0c1307604a4d3c2a604bf3b8;p=jalview.git
diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 0e77f02..1801eb1 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -1,5 +1,5 @@
/*
- * 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.
@@ -17,23 +17,31 @@
*/
package jalview.bin;
-import jalview.api.SequenceStructureBinding;
import jalview.appletgui.AlignFrame;
import jalview.appletgui.EmbmenuFrame;
import jalview.appletgui.FeatureSettings;
import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentOrder;
+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.JSFunctionExec;
+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;
@@ -42,11 +50,11 @@ import java.awt.event.WindowAdapter;
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;
+import netscape.javascript.JSObject;
+
/**
* Jalview Applet. Runs in Java 1.18 runtime
*
@@ -60,8 +68,8 @@ public class JalviewLite extends Applet
// The following public methods maybe called
// externally, eg via javascript in HTML page
/**
- * @return String list of selected sequence IDs, each terminated by "¬"
- * (¬)
+ * @return String list of selected sequence IDs, each terminated by the
+ * 'boolean not' character (""+0x00AC) or (¬)
*/
public String getSelectedSequences()
{
@@ -71,8 +79,8 @@ public class JalviewLite extends Applet
/**
* @param sep
* separator string or null for default
- * @return String list of selected sequence IDs, each terminated by sep or
- * ("¬" as default)
+ * @return String list of selected sequence IDs, each terminated by given
+ * separator string
*/
public String getSelectedSequences(String sep)
{
@@ -82,12 +90,13 @@ public class JalviewLite extends Applet
/**
* @param alf
* alignframe containing selection
- * @return String list of selected sequence IDs, each terminated by "¬"
+ * @return String list of selected sequence IDs, each terminated by current
+ * default separator sequence
*
*/
public String getSelectedSequencesFrom(AlignFrame alf)
{
- return getSelectedSequencesFrom(alf, "¬");
+ return getSelectedSequencesFrom(alf, separator); // ""+0x00AC);
}
/**
@@ -96,7 +105,7 @@ public class JalviewLite extends Applet
* @param alf
* window containing selection
* @param sep
- * separator string to use - default is "¬"
+ * separator string to use - default is 'boolean not'
* @return String list of selected sequence IDs, each terminated by the given
* separator
*/
@@ -105,7 +114,7 @@ public class JalviewLite extends Applet
StringBuffer result = new StringBuffer("");
if (sep == null || sep.length() == 0)
{
- sep = "¬";
+ sep = separator; // "+0x00AC;
}
if (alf.viewport.getSelectionGroup() != null)
{
@@ -123,6 +132,327 @@ public class JalviewLite extends Applet
}
/**
+ *
+ * @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)
+ {
+ highlightIn(getDefaultTargetFrame(), 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 highlightIn(AlignFrame alf, String sequenceId,
+ String position, String alignedPosition)
+ {
+ // TODO: could try to highlight in all alignments if alf==null
+ jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
+ alf.viewport.getAlignment().getSequencesArray());
+ SequenceI sq = matcher.findIdMatch(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), null);
+ }
+ else
+ {
+ StructureSelectionManager.getStructureSelectionManager()
+ .mouseOverVamsasSequence(sq, apos, null);
+ }
+
+ }
+ }
+
+ /**
+ * 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)
+ {
+ selectIn(getDefaultTargetFrame(), sequenceIds, columns, separator);
+ }
+
+ /**
+ * 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)
+ {
+ selectIn(getDefaultTargetFrame(), 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 selectIn(AlignFrame alf, String sequenceIds, String columns)
+ {
+ selectIn(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 selectIn(AlignFrame alf, String sequenceIds, String columns,
+ String sep)
+ {
+ if (sep == null || sep.length() == 0)
+ {
+ sep = separator;
+ }
+ else
+ {
+ if (debug)
+ {
+ System.err.println("Selecting region using separator string '"
+ + 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();
+ jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
+ alf.viewport.getAlignment().getSequencesArray());
+ int start = 0, end = al.getWidth(), alw = al.getWidth();
+ boolean seqsfound = true;
+ if (ids != null && ids.length > 0)
+ {
+ seqsfound = false;
+ for (int i = 0; i < ids.length; i++)
+ {
+ if (ids[i].trim().length() == 0)
+ {
+ continue;
+ }
+ SequenceI sq = matcher.findIdMatch(ids[i]);
+ if (sq != null)
+ {
+ seqsfound = true;
+ sel.addSequence(sq, false);
+ }
+ }
+ }
+ boolean inseqpos = 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)
+ {
+ if (cl.toLowerCase().equals("sequence"))
+ {
+ // we are in the dataset sequence's coordinate frame.
+ inseqpos = true;
+ }
+ else
+ {
+ 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 + "]");
+ }
+ }
+ }
+ }
+ if (seqsfound)
+ {
+ // we only propagate the selection when it was the null selection, or the
+ // given sequences were found in the alignment.
+ if (inseqpos && sel.getSize() > 0)
+ {
+ // assume first sequence provides reference frame ?
+ SequenceI rs = sel.getSequenceAt(0);
+ start = rs.findIndex(start);
+ end = rs.findIndex(end);
+ if (csel != null)
+ {
+ Vector cs = csel.getSelected();
+ csel.clear();
+ for (int csi = 0, csiS = cs.size(); csi < csiS; csi++)
+ {
+ csel.addElement(rs.findIndex(((Integer) cs.elementAt(csi))
+ .intValue()));
+ }
+ }
+ }
+ 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
*
@@ -137,8 +467,8 @@ public class JalviewLite extends Applet
*/
public String getSelectedSequencesAsAlignment(String format, String suffix)
{
- return getSelectedSequencesAsAlignmentFrom(currentAlignFrame, format,
- suffix);
+ return getSelectedSequencesAsAlignmentFrom(getDefaultTargetFrame(),
+ format, suffix);
}
/**
@@ -175,6 +505,86 @@ public class JalviewLite extends Applet
return "";
}
+ public String getAlignmentOrder()
+ {
+ return getAlignmentOrderFrom(getDefaultTargetFrame());
+ }
+
+ public String getAlignmentOrderFrom(AlignFrame alf)
+ {
+ return getAlignmentOrderFrom(alf, separator);
+ }
+
+ public String getAlignmentOrderFrom(AlignFrame alf, String sep)
+ {
+ AlignmentI alorder = alf.getAlignViewport().getAlignment();
+ String[] order = new String[alorder.getHeight()];
+ for (int i = 0; i < order.length; i++)
+ {
+ order[i] = alorder.getSequenceAt(i).getName();
+ }
+ return arrayToSeparatorList(order);
+ }
+
+ public String orderBy(String order, String undoName)
+ {
+ return orderBy(order, undoName, separator);
+ }
+
+ public String orderBy(String order, String undoName, String sep)
+ {
+ return orderAlignmentBy(getDefaultTargetFrame(), order, undoName, sep);
+ }
+
+ public String orderAlignmentBy(AlignFrame alf, String order,
+ String undoName, String sep)
+ {
+ String[] ids = separatorListToArray(order, sep);
+ SequenceI[] sqs = null;
+ if (ids != null && ids.length > 0)
+ {
+ jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
+ alf.viewport.getAlignment().getSequencesArray());
+ int s = 0;
+ sqs = new SequenceI[ids.length];
+ for (int i = 0; i < ids.length; i++)
+ {
+ if (ids[i].trim().length() == 0)
+ {
+ continue;
+ }
+ SequenceI sq = matcher.findIdMatch(ids[i]);
+ if (sq != null)
+ {
+ sqs[s++] = sq;
+ }
+ }
+ if (s > 0)
+ {
+ SequenceI[] sqq = new SequenceI[s];
+ System.arraycopy(sqs, 0, sqq, 0, s);
+ sqs = sqq;
+ }
+ else
+ {
+ sqs = null;
+ }
+ }
+ if (sqs == null)
+ {
+ return "";
+ }
+ ;
+ AlignmentOrder aorder = new AlignmentOrder(sqs);
+
+ if (undoName != null && undoName.trim().length() == 0)
+ {
+ undoName = null;
+ }
+
+ return alf.sortBy(aorder, undoName) ? "true" : "";
+ }
+
public String getAlignment(String format)
{
return getAlignmentFrom(getDefaultTargetFrame(), format, "true");
@@ -295,6 +705,199 @@ public class JalviewLite extends Applet
return null;
}
+ public void setMouseoverListener(String listener)
+ {
+ setMouseoverListener(currentAlignFrame, listener);
+ }
+
+ private Vector javascriptListeners = 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);
+ javascriptListeners.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 " + javascriptListeners.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);
+ javascriptListeners.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 " + javascriptListeners.size()
+ + " listeners in total.");
+ }
+ }
+
+ public void setStructureListener(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.MouseOverStructureListener mol = new jalview.javascript.MouseOverStructureListener(this, listener);
+ javascriptListeners.addElement(mol);
+ StructureSelectionManager.getStructureSelectionManager()
+ .addStructureViewerListener(mol);
+ if (debug)
+ {
+ System.err.println("Added a javascript structure viewer listener '"+listener+"'");
+ System.err.println("There are now " + javascriptListeners.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 = javascriptListeners.size(); ms < msSize;)
+ {
+ Object lstn = javascriptListeners.elementAt(ms);
+ JsCallBack lstner = (JsCallBack) lstn;
+ if ((af == null || lstner.getAlignFrame() == af)
+ && (listener == null || lstner.getListenerFunction().equals(
+ listener)))
+ {
+ javascriptListeners.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 " + javascriptListeners.size()
+ + " listeners in total.");
+ }
+ }
+
+ public void stop()
+ {
+ if (javascriptListeners != null)
+ {
+ while (javascriptListeners.size() > 0)
+ {
+ Object mol = javascriptListeners.elementAt(0);
+ javascriptListeners.removeElement(mol);
+ if (mol instanceof SelectionListener)
+ {
+ StructureSelectionManager.getStructureSelectionManager()
+ .removeSelectionListener((SelectionListener) mol);
+ }
+ else
+ {
+ StructureSelectionManager.getStructureSelectionManager()
+ .removeStructureViewerListener(mol, null);
+ }
+ }
+ }
+ jalview.javascript.JSFunctionExec.stopQueue();
+ }
+
+ /**
+ * 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(String pdbResNum, String chain, String pdbfile)
+ {
+ try {
+ StructureSelectionManager.getStructureSelectionManager()
+ .mouseOverStructure(new Integer(pdbResNum).intValue(), chain, pdbfile);
+ if (debug)
+ {
+ System.err.println("mouseOver for '"+pdbResNum+"' in chain '"+chain+"' in structure '"+pdbfile+"'");
+ }
+ } catch (NumberFormatException e)
+ {
+ System.err.println("Ignoring invalid residue number string '"+pdbResNum+"'");
+ }
+ }
+
// //////////////////////////////////////////////
// //////////////////////////////////////////////
@@ -314,7 +917,7 @@ public class JalviewLite extends Applet
* AlignFrame if the applet is started as embedded on the page and then
* afterwards a new view is created.
*/
- public static AlignFrame currentAlignFrame = null;
+ public AlignFrame currentAlignFrame = null;
/**
* This is the first frame to be displayed, and does not change. API calls
@@ -332,6 +935,13 @@ public class JalviewLite extends Applet
public boolean jmolAvailable = false;
+ private boolean alignPdbStructures = false;
+
+ /**
+ * use an external structure viewer exclusively (no jmols or MCViews will be opened by JalviewLite itself)
+ */
+ public boolean useXtrnalSviewer=false;
+
public static boolean debug = false;
static String builddate = null, version = null;
@@ -382,12 +992,36 @@ public class JalviewLite extends Applet
return version;
}
+ // public JSObject scriptObject = null;
+
/**
* init method for Jalview Applet
*/
public void init()
{
+ // remove any handlers that might be hanging around from an earlier instance
+ try
+ {
+ if (debug)
+ {
+ System.err.println("Applet context is '"
+ + getAppletContext().getClass().toString() + "'");
+ }
+ JSObject scriptObject = JSObject.getWindow(this);
+ if (debug && scriptObject != null)
+ {
+ System.err.println("Applet has Javascript callback support.");
+ }
+ } catch (Exception ex)
+ {
+ System.err
+ .println("Warning: No JalviewLite javascript callbacks available.");
+ if (debug)
+ {
+ ex.printStackTrace();
+ }
+ }
/**
* turn on extra applet debugging
*/
@@ -403,6 +1037,11 @@ public class JalviewLite extends Applet
System.err.println("Build Date : " + getBuildDate());
}
+ String externalsviewer = getParameter("externalstructureviewer");
+ if (externalsviewer!=null)
+ {
+ useXtrnalSviewer=externalsviewer.trim().toLowerCase().equals("true");
+ }
/**
* if true disable the check for jmol
*/
@@ -450,14 +1089,13 @@ public class JalviewLite extends Applet
b = 255;
}
}
-
param = getParameter("label");
if (param != null)
{
launcher.setLabel(param);
}
- this.setBackground(new Color(r, g, b));
+ setBackground(new Color(r, g, b));
file = getParameter("file");
@@ -477,13 +1115,13 @@ public class JalviewLite extends Applet
}
}
- final JalviewLite applet = this;
+ final JalviewLite jvapplet = this;
if (getParameter("embedded") != null
&& getParameter("embedded").equalsIgnoreCase("true"))
{
// Launch as embedded applet in page
embedded = true;
- LoadingThread loader = new LoadingThread(file, applet);
+ LoadingThread loader = new LoadingThread(file, jvapplet);
loader.start();
}
else if (file != null)
@@ -497,7 +1135,7 @@ public class JalviewLite extends Applet
{
public void actionPerformed(ActionEvent e)
{
- LoadingThread loader = new LoadingThread(file, applet);
+ LoadingThread loader = new LoadingThread(file, jvapplet);
loader.start();
}
});
@@ -505,7 +1143,7 @@ public class JalviewLite extends Applet
else
{
// Open jalviewLite immediately.
- LoadingThread loader = new LoadingThread(file, applet);
+ LoadingThread loader = new LoadingThread(file, jvapplet);
loader.start();
}
}
@@ -515,6 +1153,48 @@ public class JalviewLite extends Applet
// still be called to open new alignments.
file = "NO FILE";
fileFound = false;
+ // callInitCallback();
+ }
+ }
+
+ private void callInitCallback()
+ {
+ String initjscallback = getParameter("oninit");
+ if (initjscallback == null)
+ {
+ return;
+ }
+ initjscallback = initjscallback.trim();
+ if (initjscallback.length() > 0)
+ {
+ JSObject scriptObject = null;
+ try
+ {
+ scriptObject = JSObject.getWindow(this);
+ } catch (Exception ex)
+ {
+ }
+ ;
+ if (scriptObject != null)
+ {
+ try
+ {
+ // do onInit with the JS executor thread
+ new JSFunctionExec(this).executeJavascriptFunction(true,
+ initjscallback, null, "Calling oninit callback '"
+ + initjscallback + "'.");
+ } catch (Exception e)
+ {
+ System.err.println("Exception when executing _oninit callback '"
+ + initjscallback + "'.");
+ e.printStackTrace();
+ }
+ }
+ else
+ {
+ System.err.println("Not executing _oninit callback '"
+ + initjscallback + "' - no scripting allowed.");
+ }
}
}
@@ -545,10 +1225,10 @@ public class JalviewLite extends Applet
if (frame instanceof AlignFrame)
{
((AlignFrame) frame).closeMenuItem_actionPerformed();
- }
- if (currentAlignFrame == frame)
- {
- currentAlignFrame = null;
+ if (((AlignFrame) frame).viewport.applet.currentAlignFrame == frame)
+ {
+ ((AlignFrame) frame).viewport.applet.currentAlignFrame = null;
+ }
}
lastFrameX -= 40;
lastFrameY -= 40;
@@ -564,7 +1244,7 @@ public class JalviewLite extends Applet
{
if (frame instanceof AlignFrame)
{
- currentAlignFrame = (AlignFrame) frame;
+ ((AlignFrame) frame).viewport.applet.currentAlignFrame = (AlignFrame) frame;
if (debug)
{
System.err.println("Activated window " + frame);
@@ -612,9 +1292,32 @@ public class JalviewLite extends Applet
{
g.setColor(Color.black);
g.setFont(new Font("Arial", Font.BOLD, 24));
- g.drawString("Jalview Applet", 50, this.getSize().height / 2 - 30);
- g.drawString("Loading Data...", 50, this.getSize().height / 2);
+ g.drawString("Jalview Applet", 50, getSize().height / 2 - 30);
+ g.drawString("Loading Data...", 50, getSize().height / 2);
+ }
+ }
+
+ /**
+ * 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;
}
class LoadJmolThread extends Thread
@@ -743,6 +1446,7 @@ public class JalviewLite extends Applet
;
}
startLoading();
+ // applet.callInitCallback();
}
private void startLoading()
@@ -796,7 +1500,8 @@ public class JalviewLite extends Applet
if (protocol == jalview.io.AppletFormatAdapter.PASTE)
{
- newAlignFrame.setTitle("Sequences from " + getDocumentBase());
+ newAlignFrame.setTitle("Sequences from "
+ + applet.getDocumentBase());
}
newAlignFrame.statusBar.setText("Successfully loaded file " + file);
@@ -837,7 +1542,7 @@ public class JalviewLite extends Applet
}
}
- String param = getParameter("features");
+ String param = applet.getParameter("features");
if (param != null)
{
param = setProtocolState(param);
@@ -845,14 +1550,14 @@ public class JalviewLite extends Applet
newAlignFrame.parseFeaturesFile(param, protocol);
}
- param = getParameter("showFeatureSettings");
+ param = applet.getParameter("showFeatureSettings");
if (param != null && param.equalsIgnoreCase("true"))
{
newAlignFrame.viewport.showSequenceFeatures(true);
new FeatureSettings(newAlignFrame.alignPanel);
}
- param = getParameter("annotations");
+ param = applet.getParameter("annotations");
if (param != null)
{
param = setProtocolState(param);
@@ -872,7 +1577,7 @@ public class JalviewLite extends Applet
}
- param = getParameter("jnetfile");
+ param = applet.getParameter("jnetfile");
if (param != null)
{
try
@@ -896,7 +1601,12 @@ public class JalviewLite extends Applet
ex.printStackTrace();
}
}
-
+ /*
+ * Undocumented for 2.6
+ * - related to JAL-434
+ */
+ applet.setAlignPdbStructures(getDefaultParameter("alignpdbfiles",
+ false));
/*
*
@@ -907,12 +1617,19 @@ public class JalviewLite extends Applet
*/
int pdbFileCount = 0;
+ // Accumulate pdbs here if they are heading for the same view (if
+ // alignPdbStructures is true)
+ Vector pdbs = new Vector();
+ // create a lazy matcher if we're asked to
+ jalview.analysis.SequenceIdMatcher matcher = (applet.getDefaultParameter("relaxedidmatch", false)) ? new jalview.analysis.SequenceIdMatcher(
+ newAlignFrame.getAlignViewport().getAlignment().getSequencesArray()) : null;
+
do
{
if (pdbFileCount > 0)
- param = getParameter("PDBFILE" + pdbFileCount);
+ param = applet.getParameter("PDBFILE" + pdbFileCount);
else
- param = getParameter("PDBFILE");
+ param = applet.getParameter("PDBFILE");
if (param != null)
{
@@ -929,8 +1646,8 @@ public class JalviewLite extends Applet
String sequence = applet.getParameter("PDBSEQ");
if (sequence != null)
seqs = new SequenceI[]
- { (Sequence) newAlignFrame.getAlignViewport()
- .getAlignment().findName(sequence) };
+ { matcher==null ? (Sequence) newAlignFrame.getAlignViewport()
+ .getAlignment().findName(sequence) : matcher.findIdMatch(sequence) };
}
else
@@ -949,8 +1666,8 @@ public class JalviewLite extends Applet
tmp2.addElement(st2.nextToken());
seqstring = st2.nextToken();
}
- tmp.addElement((Sequence) newAlignFrame.getAlignViewport()
- .getAlignment().findName(seqstring));
+ tmp.addElement(matcher==null ? (Sequence) newAlignFrame.getAlignViewport()
+ .getAlignment().findName(seqstring) : matcher.findIdMatch(seqstring));
}
seqs = new SequenceI[tmp.size()];
@@ -999,26 +1716,50 @@ public class JalviewLite extends Applet
}
}
- newAlignFrame.newStructureView(applet, pdb, seqs, chains,
- protocol);
-
+ if (!alignPdbStructures)
+ {
+ newAlignFrame.newStructureView(applet, pdb, seqs, chains,
+ protocol);
+ }
+ else
+ {
+ 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
//
// hide specific groups
- param = getParameter("hidefeaturegroups");
+ param = applet.getParameter("hidefeaturegroups");
if (param != null)
{
applet.setFeatureGroupStateOn(newAlignFrame, param, false);
}
// show specific groups
- param = getParameter("showfeaturegroups");
+ param = applet.getParameter("showfeaturegroups");
if (param != null)
{
applet.setFeatureGroupStateOn(newAlignFrame, param, true);
@@ -1027,8 +1768,8 @@ public class JalviewLite extends Applet
else
{
fileFound = false;
- remove(launcher);
- repaint();
+ applet.remove(launcher);
+ applet.repaint();
}
}
@@ -1064,7 +1805,7 @@ public class JalviewLite extends Applet
{
if (file.indexOf("://") == -1)
{
- file = getCodeBase() + file;
+ file = applet.getCodeBase() + file;
if (debug)
{
System.err.println("Prepended codebase for resource: '" + file
@@ -1081,7 +1822,7 @@ public class JalviewLite extends Applet
* return null with an error message on System.err indicating the
* fact.
*/
- protected AlignFrame getDefaultTargetFrame()
+ public AlignFrame getDefaultTargetFrame()
{
if (currentAlignFrame != null)
{
@@ -1099,9 +1840,9 @@ public class JalviewLite extends Applet
/**
* separator used for separatorList
*/
- protected String separator = "|"; // this is a safe(ish) separator - tabs
-
- // don't work for firefox
+ protected String separator = "" + ((char) 0x00AC); // the default used to be
+ // '|' but many sequence
+ // IDS include pipes.
/**
* parse the string into a list
@@ -1111,8 +1852,21 @@ public class JalviewLite extends Applet
*/
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;
@@ -1123,7 +1877,11 @@ public class JalviewLite extends Applet
}
if (cp < list.length())
{
- jv.addElement(list.substring(cp));
+ String c = list.substring(cp);
+ if (!c.equals(separator))
+ {
+ jv.addElement(c);
+ }
}
if (jv.size() > 0)
{
@@ -1160,20 +1918,31 @@ public class JalviewLite extends Applet
*/
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++)
+ for (int i = 0, iSize = list.length; i < iSize; i++)
{
if (list[i] != null)
{
+ if (i > 0)
+ {
+ v.append(separator);
+ }
v.append(list[i]);
}
- v.append(separator);
- }
- if (list[list.length - 1] != null)
- {
- v.append(list[list.length - 1]);
}
if (debug)
{
@@ -1188,7 +1957,7 @@ public class JalviewLite extends Applet
System.err.println("Returning empty '" + separator
+ "' separated List\n");
}
- return "";
+ return "" + separator;
}
/**
@@ -1272,11 +2041,20 @@ public class JalviewLite extends Applet
* List separator string
*
* @param separator
- * the separator to set
+ * the separator to set. empty string will reset separator to default
*/
public void setSeparator(String separator)
{
+ if (separator == null || separator.length() < 1)
+ {
+ // reset to default
+ separator = "" + ((char) 0x00AC);
+ }
this.separator = separator;
+ if (debug)
+ {
+ System.err.println("Default Separator now: '" + separator + "'");
+ }
}
/**
@@ -1325,6 +2103,20 @@ public class JalviewLite extends Applet
return alFrame.addPdbFile(sequenceId, pdbEntryString, pdbFile);
}
+ protected void setAlignPdbStructures(boolean alignPdbStructures)
+ {
+ this.alignPdbStructures = alignPdbStructures;
+ }
+
+ public boolean isAlignPdbStructures()
+ {
+ return alignPdbStructures;
+ }
+
+ public void start()
+ {
+ callInitCallback();
+ }
/**
* bind structures in a viewer to any matching sequences in an alignFrame (use
@@ -1334,21 +2126,13 @@ public class JalviewLite extends Applet
* @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; }
*/
}