/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
package jalview.bin;
-import java.applet.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.util.*;
-
-import jalview.appletgui.*;
-import jalview.datamodel.*;
-import jalview.io.*;
+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.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;
+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.StringTokenizer;
+import java.util.Vector;
+
+import netscape.javascript.JSObject;
/**
* Jalview Applet. Runs in Java 1.18 runtime
// 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()
/**
* @param sep
- * separator string or null for default
- * @return String list of selected sequence IDs, each terminated by sep or
- * ("¬" as default)
+ * separator string or null for default
+ * @return String list of selected sequence IDs, each terminated by given separator string
*/
public String getSelectedSequences(String sep)
{
/**
* @param alf
- * alignframe containing selection
- * @return String list of selected sequence IDs, each terminated by "¬"
+ * alignframe containing selection
+ * @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);
}
/**
* get list of selected sequence IDs separated by given separator
*
* @param alf
- * window containing selection
+ * 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
*/
StringBuffer result = new StringBuffer("");
if (sep == null || sep.length() == 0)
{
- sep = "¬";
+ sep = separator; // "+0x00AC;
}
if (alf.viewport.getSelectionGroup() != null)
{
}
/**
+ *
+ * @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
+ 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), 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();
+ 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
*
- * @param alf -
- * where selection is
- * @param format -
- * format of alignment file
- * @param suffix -
- * "true" to append /start-end string to each sequence ID
+ * @param alf
+ * - where selection is
+ * @param format
+ * - format of alignment file
+ * @param suffix
+ * - "true" to append /start-end string to each sequence ID
* @return selected sequences as flat file or empty string if there was no
* current selection
*/
public String getSelectedSequencesAsAlignment(String format, String suffix)
{
- return getSelectedSequencesAsAlignmentFrom(currentAlignFrame, format,
+ return getSelectedSequencesAsAlignmentFrom(getDefaultTargetFrame(), format,
suffix);
}
* get sequences selected in alf and return their alignment in format 'format'
* either with or without suffix
*
- * @param alf -
- * where selection is
- * @param format -
- * format of alignment file
- * @param suffix -
- * "true" to append /start-end string to each sequence ID
+ * @param alf
+ * - where selection is
+ * @param format
+ * - format of alignment file
+ * @param suffix
+ * - "true" to append /start-end string to each sequence ID
* @return selected sequences as flat file or empty string if there was no
* current selection
*/
/**
*
* @param text
- * alignment file as a string
+ * alignment file as a string
* @param title
- * window title
+ * window title
* @return null or new alignment frame
*/
public AlignFrame loadAlignment(String text, String title)
{
Alignment al = null;
-
+
String format = new IdentifyFile().Identify(text,
AppletFormatAdapter.PASTE);
try
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);
+ }
+ }
+ }
+ 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(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;
* 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
* will default to this instance if currentAlignFrame is null.
*/
- AlignFrame initialAlignFrame=null;
+ AlignFrame initialAlignFrame = null;
boolean embedded = false;
private boolean checkForJmol = true;
- private boolean checkedForJmol = false; // ensure we don't check for jmol every time the app is re-inited
+
+ private boolean checkedForJmol = false; // ensure we don't check for jmol
+
+ // every time the app is re-inited
public boolean jmolAvailable = false;
- public static boolean debug=false;
+ private boolean alignPdbStructures = false;
+
+ public static boolean debug = false;
+
+ static String builddate = null, version = null;
+
+ private static void initBuildDetails()
+ {
+ if (builddate == null)
+ {
+ builddate = "unknown";
+ version = "test";
+ java.net.URL url = JalviewLite.class
+ .getResource("/.build_properties");
+ if (url != null)
+ {
+ try
+ {
+ BufferedReader reader = new BufferedReader(new InputStreamReader(
+ url.openStream()));
+ String line;
+ while ((line = reader.readLine()) != null)
+ {
+ if (line.indexOf("VERSION") > -1)
+ {
+ version = line.substring(line.indexOf("=") + 1);
+ }
+ if (line.indexOf("BUILD_DATE") > -1)
+ {
+ builddate = line.substring(line.indexOf("=") + 1);
+ }
+ }
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ }
+ }
+
+ public static String getBuildDate()
+ {
+ initBuildDetails();
+ return builddate;
+ }
+
+ public static String getVersion()
+ {
+ initBuildDetails();
+ 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
*/
{
debug = dbg.toLowerCase().equals("true");
}
+ if (debug)
+ {
+
+ System.err.println("JalviewLite Version " + getVersion());
+ System.err.println("Build Date : " + getBuildDate());
+
+ }
/**
* if true disable the check for jmol
*/
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");
if (file == null)
}
}
- 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)
{
if (getParameter("showbutton") == null
- || !getParameter("showbutton").equalsIgnoreCase("false"))
+ || !getParameter("showbutton").equalsIgnoreCase(
+ "false"))
{
// Add the JalviewLite 'Button' to the page
add(launcher);
{
public void actionPerformed(ActionEvent e)
{
- LoadingThread loader = new LoadingThread(file, applet);
+ LoadingThread loader = new LoadingThread(file, jvapplet);
loader.start();
}
});
else
{
// Open jalviewLite immediately.
- LoadingThread loader = new LoadingThread(file, applet);
+ LoadingThread loader = new LoadingThread(file, jvapplet);
loader.start();
}
}
// 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.");
+ }
}
}
* Initialises and displays a new java.awt.Frame
*
* @param frame
- * java.awt.Frame to be displayed
+ * java.awt.Frame to be displayed
* @param title
- * title of new frame
+ * title of new frame
* @param width
- * width if new frame
+ * width if new frame
* @param height
- * height of new frame
+ * height of new frame
*/
public static void addFrame(final Frame frame, String title, int width,
int height)
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;
{
if (frame instanceof AlignFrame)
{
- currentAlignFrame = (AlignFrame) frame;
+ ((AlignFrame) frame).viewport.applet.currentAlignFrame = (AlignFrame) frame;
if (debug)
{
System.err.println("Activated window " + frame);
/*
* Probably not necessary to do this - see TODO above. (non-Javadoc)
*
- * @see java.awt.event.WindowAdapter#windowDeactivated(java.awt.event.WindowEvent)
+ * @see
+ * java.awt.event.WindowAdapter#windowDeactivated(java.awt.event.WindowEvent
+ * )
*
* public void windowDeactivated(WindowEvent e) { if (currentAlignFrame ==
* frame) { currentAlignFrame = null; if (debug) {
* If file given in parameter not found, displays error message
*
* @param g
- * graphics context
+ * graphics context
*/
public void paint(Graphics g)
{
{
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
{
- private boolean running=false;
+ private boolean running = false;
public void run()
{
- if (running || checkedForJmol) {
+ if (running || checkedForJmol)
+ {
return;
}
- running=true;
+ running = true;
if (checkForJmol)
{
try
.println("Skipping Jmol check. Will use MCView (probably)");
}
}
- checkedForJmol=true;
- running=false;
+ checkedForJmol = true;
+ running = false;
}
public boolean notFinished()
* State variable: format of file source
*/
String format;
+
String _file;
+
JalviewLite applet;
+
private void dbgMsg(String msg)
{
if (applet.debug)
dbgMsg("Protocol identified as '" + protocol + "'");
return file;
}
-
+
public LoadingThread(String _file, JalviewLite _applet)
{
- this._file=_file;
+ this._file = _file;
applet = _applet;
}
while (jmolchecker.notFinished())
{
// wait around until the Jmol check is complete.
- try { Thread.sleep(2); } catch (Exception e) {};
+ try
+ {
+ Thread.sleep(2);
+ } catch (Exception e)
+ {
+ }
+ ;
}
startLoading();
+ // applet.callInitCallback();
}
private void startLoading()
{
dbgMsg("File load exception.");
ex.printStackTrace();
- if (debug) {
- try {
+ if (debug)
+ {
+ try
+ {
FileParse fp = new FileParse(file, protocol);
String ln = null;
- dbgMsg(">>>Dumping contents of '"+file+"' "+"("+protocol+")");
- while ((ln=fp.nextLine())!=null) {
+ dbgMsg(">>>Dumping contents of '" + file + "' " + "("
+ + protocol + ")");
+ while ((ln = fp.nextLine()) != null)
+ {
dbgMsg(ln);
}
dbgMsg(">>>Dump finished.");
} catch (Exception e)
{
- System.err.println("Exception when trying to dump the content of the file parameter.");
+ System.err
+ .println("Exception when trying to dump the content of the file parameter.");
e.printStackTrace();
}
}
{
dbgMsg("Successfully loaded file.");
newAlignFrame = new AlignFrame(al, applet, file, embedded);
- if (initialAlignFrame==null)
+ if (initialAlignFrame == null)
{
initialAlignFrame = newAlignFrame;
}
if (protocol == jalview.io.AppletFormatAdapter.PASTE)
{
- newAlignFrame.setTitle("Sequences from " + getDocumentBase());
+ newAlignFrame.setTitle("Sequences from "
+ + applet.getDocumentBase());
}
- newAlignFrame.statusBar.setText("Successfully loaded file "
- + file);
+ newAlignFrame.statusBar.setText("Successfully loaded file " + file);
String treeFile = applet.getParameter("tree");
if (treeFile == null)
}
}
- String param = getParameter("features");
+ String param = applet.getParameter("features");
if (param != null)
{
param = setProtocolState(param);
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);
if (new AnnotationFile().readAnnotationFile(
- newAlignFrame.viewport.getAlignment(), param,
- protocol))
+ newAlignFrame.viewport.getAlignment(), param, protocol))
{
newAlignFrame.alignPanel.fontChanged();
newAlignFrame.alignPanel.setScrollValues(0, 0);
}
- param = getParameter("jnetfile");
+ param = applet.getParameter("jnetfile");
if (param != null)
{
try
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)
- param = getParameter("PDBFILE" + pdbFileCount);
+ param = applet.getParameter("PDBFILE" + pdbFileCount);
else
- param = getParameter("PDBFILE");
+ param = applet.getParameter("PDBFILE");
if (param != null)
{
tmp2.addElement(st2.nextToken());
seqstring = st2.nextToken();
}
- tmp.addElement((Sequence) newAlignFrame
- .getAlignViewport().getAlignment().findName(
- seqstring));
+ tmp.addElement((Sequence) newAlignFrame.getAlignViewport()
+ .getAlignment().findName(seqstring));
}
seqs = new SequenceI[tmp.size()];
// 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
//
// hide specific groups
- param = getParameter("hidefeaturegroups");
+ param = applet.getParameter("hidefeaturegroups");
if (param != null)
{
- applet.setFeatureGroupStateOn(newAlignFrame,param, false);
+ applet.setFeatureGroupStateOn(newAlignFrame, param, false);
}
// show specific groups
- param = getParameter("showfeaturegroups");
+ param = applet.getParameter("showfeaturegroups");
if (param != null)
{
- applet.setFeatureGroupStateOn(newAlignFrame,param, true);
+ applet.setFeatureGroupStateOn(newAlignFrame, param, true);
}
}
else
{
fileFound = false;
- remove(launcher);
- repaint();
+ applet.remove(launcher);
+ applet.repaint();
}
}
* Discovers whether the given file is in the Applet Archive
*
* @param file
- * String
+ * String
* @return boolean
*/
boolean inArchive(String file)
{
if (file.indexOf("://") == -1)
{
- file = getCodeBase() + file;
+ file = applet.getCodeBase() + file;
if (debug)
{
System.err.println("Prepended codebase for resource: '" + file
* return null with an error message on System.err indicating the
* fact.
*/
- protected AlignFrame getDefaultTargetFrame()
+ public AlignFrame getDefaultTargetFrame()
{
if (currentAlignFrame != null)
{
/**
* 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
*
*/
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;
}
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)
{
*/
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)
{
System.err.println("Returning empty '" + separator
+ "' separated List\n");
}
- return "";
+ return "" + separator;
}
/**
/**
* @param alf
- * alignframe to get feature groups on
+ * alignframe to get feature groups on
* @return
* @see jalview.appletgui.AlignFrame#getFeatureGroups()
*/
/**
* @param alf
- * align frame to get groups of state visible
+ * align frame to get groups of state visible
* @param visible
* @return
* @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)
/**
* @param groups
- * tab separated list of group names
+ * tab separated list of group names
* @param state
- * true or false
+ * true or false
* @see jalview.appletgui.AlignFrame#setFeatureGroupState(java.lang.String[],
* boolean)
*/
* 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+"'");
+ }
}
+
+ /**
+ * get boolean value of applet parameter 'name' and return default if
+ * parameter is not set
+ *
+ * @param name
+ * name of paremeter
+ * @param def
+ * the value to return otherwise
+ * @return true or false
+ */
+ public boolean getDefaultParameter(String name, boolean def)
+ {
+ String stn;
+ if ((stn = getParameter(name)) == null)
+ {
+ return def;
+ }
+ if (stn.toLowerCase().equals("true"))
+ {
+ return true;
+ }
+ 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;
+ }
+
+ public void start()
+ {
+ callInitCallback();
+ }
+
+ /**
+ * 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