X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=33ff254843809cd69fed6e15972bc8b296394612;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=dd2bf70a64c2ed367ffedc02ce7cad0112e272f8;hpb=caf13e6a9dc82023cd8648420201e5ad60ce0393;p=jalview.git
diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
old mode 100755
new mode 100644
index dd2bf70..33ff254
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -1,1959 +1,2686 @@
-/*
- * 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.
- *
- * 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.
- *
- * 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 .
- */
-package jalview.bin;
-
-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
- *
- * @author $author$
- * @version $Revision$
- */
-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 the 'boolean not' character (""+0x00AC) or
- * (¬)
- */
- public String getSelectedSequences()
- {
- return getSelectedSequencesFrom(getDefaultTargetFrame());
- }
-
- /**
- * @param sep
- * separator string or null for default
- * @return String list of selected sequence IDs, each terminated by given separator string
- */
- public String getSelectedSequences(String sep)
- {
- return getSelectedSequencesFrom(getDefaultTargetFrame(), sep);
- }
-
- /**
- * @param alf
- * 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,separator); // ""+0x00AC);
- }
-
- /**
- * get list of selected sequence IDs separated by given separator
- *
- * @param alf
- * window containing selection
- * @param sep
- * separator string to use - default is 'boolean not'
- * @return String list of selected sequence IDs, each terminated by the given
- * separator
- */
- public String getSelectedSequencesFrom(AlignFrame alf, String sep)
- {
- StringBuffer result = new StringBuffer("");
- if (sep == null || sep.length() == 0)
- {
- sep = separator; // "+0x00AC;
- }
- if (alf.viewport.getSelectionGroup() != null)
- {
- SequenceI[] seqs = alf.viewport.getSelectionGroup()
- .getSequencesInOrder(alf.viewport.getAlignment());
-
- for (int i = 0; i < seqs.length; i++)
- {
- result.append(seqs[i].getName());
- result.append(sep);
- }
- }
-
- return result.toString();
- }
-
- /**
- *
- * @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
- * @return selected sequences as flat file or empty string if there was no
- * current selection
- */
- public String getSelectedSequencesAsAlignment(String format, String suffix)
- {
- 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
- * @return selected sequences as flat file or empty string if there was no
- * current selection
- */
- public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
- String format, String suffix)
- {
- try
- {
- boolean seqlimits = suffix.equalsIgnoreCase("true");
- if (alf.viewport.getSelectionGroup() != null)
- {
- String reply = new AppletFormatAdapter().formatSequences(format,
- new Alignment(alf.viewport.getSelectionAsNewSequence()),
- seqlimits);
- return reply;
- }
- } catch (Exception ex)
- {
- ex.printStackTrace();
- return "Error retrieving alignment in " + format + " format. ";
- }
- return "";
- }
-
- public String getAlignment(String format)
- {
- return getAlignmentFrom(getDefaultTargetFrame(), format, "true");
- }
-
- public String getAlignmentFrom(AlignFrame alf, String format)
- {
- return getAlignmentFrom(alf, format, "true");
- }
-
- public String getAlignment(String format, String suffix)
- {
- return getAlignmentFrom(getDefaultTargetFrame(), format, suffix);
- }
-
- public String getAlignmentFrom(AlignFrame alf, String format,
- String suffix)
- {
- try
- {
- boolean seqlimits = suffix.equalsIgnoreCase("true");
-
- String reply = new AppletFormatAdapter().formatSequences(format,
- alf.viewport.getAlignment(), seqlimits);
- return reply;
- } catch (Exception ex)
- {
- ex.printStackTrace();
- return "Error retrieving alignment in " + format + " format. ";
- }
- }
-
- public void loadAnnotation(String annotation)
- {
- loadAnnotationFrom(getDefaultTargetFrame(), annotation);
- }
-
- public void loadAnnotationFrom(AlignFrame alf, String annotation)
- {
- if (new AnnotationFile().readAnnotationFile(alf.getAlignViewport()
- .getAlignment(), annotation, AppletFormatAdapter.PASTE))
- {
- alf.alignPanel.fontChanged();
- alf.alignPanel.setScrollValues(0, 0);
- }
- else
- {
- alf.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE);
- }
- }
-
- public String getFeatures(String format)
- {
- return getFeaturesFrom(getDefaultTargetFrame(), format);
- }
-
- public String getFeaturesFrom(AlignFrame alf, String format)
- {
- return alf.outputFeatures(false, format);
- }
-
- public String getAnnotation()
- {
- return getAnnotationFrom(getDefaultTargetFrame());
- }
-
- public String getAnnotationFrom(AlignFrame alf)
- {
- return alf.outputAnnotations(false);
- }
-
- public AlignFrame newView()
- {
- return newViewFrom(getDefaultTargetFrame());
- }
-
- public AlignFrame newView(String name)
- {
- return newViewFrom(getDefaultTargetFrame(), name);
- }
-
- public AlignFrame newViewFrom(AlignFrame alf)
- {
- return alf.newView(null);
- }
-
- public AlignFrame newViewFrom(AlignFrame alf, String name)
- {
- return alf.newView(name);
- }
-
- /**
- *
- * @param text
- * alignment file as a string
- * @param 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
- {
- al = new AppletFormatAdapter().readFile(text,
- AppletFormatAdapter.PASTE, format);
- if (al.getHeight() > 0)
- {
- return new AlignFrame(al, this, title, false);
- }
- } catch (java.io.IOException ex)
- {
- ex.printStackTrace();
- }
- 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);
- }
-
- // //////////////////////////////////////////////
- // //////////////////////////////////////////////
-
- public static int lastFrameX = 200;
-
- public static int lastFrameY = 200;
-
- boolean fileFound = true;
-
- String file = "No file";
-
- Button launcher = new Button("Start Jalview");
-
- /**
- * The currentAlignFrame is static, it will change if and when the user
- * selects a new window. Note that it will *never* point back to the embedded
- * AlignFrame if the applet is started as embedded on the page and then
- * afterwards a new view is created.
- */
- 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;
-
- 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
-
- public boolean jmolAvailable = 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 (getAppletContext() instanceof sun.plugin.javascript.JSContext) {
- if (debug)
- {
- System.err.println("Applet context implements JSContext - should have callback support!");
- }
- }
- JSObject scriptObject = JSObject.getWindow(this);
- } catch (Exception ex)
- {
- System.err
- .println("Warning: No JalviewLite javascript callbacks available.");
- if (debug)
- {
- ex.printStackTrace();
- }
- }
- /**
- * turn on extra applet debugging
- */
- String dbg = getParameter("debug");
- if (dbg != null)
- {
- 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
- */
- String chkforJmol = getParameter("nojmol");
- if (chkforJmol != null)
- {
- checkForJmol = !chkforJmol.equals("true");
- }
- /**
- * get the separator parameter if present
- */
- String sep = getParameter("separator");
- if (sep != null)
- {
- if (sep.length() > 0)
- {
- separator = sep;
- if (debug)
- {
- System.err.println("Separator set to '" + separator + "'");
- }
- }
- else
- {
- throw new Error(
- "Invalid separator parameter - must be non-zero length");
- }
- }
- int r = 255;
- int g = 255;
- int b = 255;
- String param = getParameter("RGB");
-
- if (param != null)
- {
- try
- {
- r = Integer.parseInt(param.substring(0, 2), 16);
- g = Integer.parseInt(param.substring(2, 4), 16);
- b = Integer.parseInt(param.substring(4, 6), 16);
- } catch (Exception ex)
- {
- r = 255;
- g = 255;
- b = 255;
- }
- }
- param = getParameter("label");
- if (param != null)
- {
- launcher.setLabel(param);
- }
-
- setBackground(new Color(r, g, b));
-
- file = getParameter("file");
-
- if (file == null)
- {
- // Maybe the sequences are added as parameters
- StringBuffer data = new StringBuffer("PASTE");
- int i = 1;
- while ((file = getParameter("sequence" + i)) != null)
- {
- data.append(file.toString() + "\n");
- i++;
- }
- if (data.length() > 5)
- {
- file = data.toString();
- }
- }
-
- 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, jvapplet);
- loader.start();
- }
- else if (file != null)
- {
- if (getParameter("showbutton") == null
- || !getParameter("showbutton").equalsIgnoreCase(
- "false"))
- {
- // Add the JalviewLite 'Button' to the page
- add(launcher);
- launcher.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- LoadingThread loader = new LoadingThread(file, jvapplet);
- loader.start();
- }
- });
- }
- else
- {
- // Open jalviewLite immediately.
- LoadingThread loader = new LoadingThread(file, jvapplet);
- loader.start();
- }
- }
- else
- {
- // jalview initialisation with no alignment. loadAlignment() method can
- // 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
- * @param title
- * title of new frame
- * @param width
- * width if new frame
- * @param height
- * height of new frame
- */
- public static void addFrame(final Frame frame, String title, int width,
- int height)
- {
- frame.setLocation(lastFrameX, lastFrameY);
- lastFrameX += 40;
- lastFrameY += 40;
- frame.setSize(width, height);
- frame.setTitle(title);
- frame.addWindowListener(new WindowAdapter()
- {
- public void windowClosing(WindowEvent e)
- {
- if (frame instanceof AlignFrame)
- {
- ((AlignFrame) frame).closeMenuItem_actionPerformed();
- if (((AlignFrame) frame).viewport.applet.currentAlignFrame == frame)
- {
- ((AlignFrame) frame).viewport.applet.currentAlignFrame = null;
- }
- }
- lastFrameX -= 40;
- lastFrameY -= 40;
- if (frame instanceof EmbmenuFrame)
- {
- ((EmbmenuFrame) frame).destroyMenus();
- }
- frame.setMenuBar(null);
- frame.dispose();
- }
-
- public void windowActivated(WindowEvent e)
- {
- if (frame instanceof AlignFrame)
- {
- ((AlignFrame) frame).viewport.applet.currentAlignFrame = (AlignFrame) frame;
- if (debug)
- {
- System.err.println("Activated window " + frame);
- }
- }
- // be good.
- super.windowActivated(e);
- }
- /*
- * Probably not necessary to do this - see TODO above. (non-Javadoc)
- *
- * @see
- * java.awt.event.WindowAdapter#windowDeactivated(java.awt.event.WindowEvent
- * )
- *
- * public void windowDeactivated(WindowEvent e) { if (currentAlignFrame ==
- * frame) { currentAlignFrame = null; if (debug) {
- * System.err.println("Deactivated window "+frame); } }
- * super.windowDeactivated(e); }
- */
- });
- frame.setVisible(true);
- }
-
- /**
- * This paints the background surrounding the "Launch Jalview button"
- *
- * If file given in parameter not found, displays error message
- *
- * @param g
- * graphics context
- */
- public void paint(Graphics g)
- {
- if (!fileFound)
- {
- g.setColor(new Color(200, 200, 200));
- g.setColor(Color.cyan);
- g.fillRect(0, 0, getSize().width, getSize().height);
- g.setColor(Color.red);
- g.drawString("Jalview can't open file", 5, 15);
- g.drawString("\"" + file + "\"", 5, 30);
- }
- else if (embedded)
- {
- g.setColor(Color.black);
- g.setFont(new Font("Arial", Font.BOLD, 24));
- 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;
-
- public void run()
- {
- if (running || checkedForJmol)
- {
- return;
- }
- running = true;
- if (checkForJmol)
- {
- try
- {
- if (!System.getProperty("java.version").startsWith("1.1"))
- {
- Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter");
- jmolAvailable = true;
- }
- if (!jmolAvailable)
- {
- System.out
- .println("Jmol not available - Using MCview for structures");
- }
- } catch (java.lang.ClassNotFoundException ex)
- {
- }
- }
- else
- {
- jmolAvailable = false;
- if (debug)
- {
- System.err
- .println("Skipping Jmol check. Will use MCView (probably)");
- }
- }
- checkedForJmol = true;
- running = false;
- }
-
- public boolean notFinished()
- {
- return running || !checkedForJmol;
- }
- }
-
- class LoadingThread extends Thread
- {
- /**
- * State variable: File source
- */
- String file;
-
- /**
- * State variable: protocol for access to file source
- */
- String protocol;
-
- /**
- * State variable: format of file source
- */
- String format;
-
- String _file;
-
- JalviewLite applet;
-
- private void dbgMsg(String msg)
- {
- if (applet.debug)
- {
- System.err.println(msg);
- }
- }
-
- /**
- * update the protocol state variable for accessing the datasource located
- * by file.
- *
- * @param file
- * @return possibly updated datasource string
- */
- public String setProtocolState(String file)
- {
- if (file.startsWith("PASTE"))
- {
- file = file.substring(5);
- protocol = AppletFormatAdapter.PASTE;
- }
- else if (inArchive(file))
- {
- protocol = AppletFormatAdapter.CLASSLOADER;
- }
- else
- {
- file = addProtocol(file);
- protocol = AppletFormatAdapter.URL;
- }
- dbgMsg("Protocol identified as '" + protocol + "'");
- return file;
- }
-
- public LoadingThread(String _file, JalviewLite _applet)
- {
- this._file = _file;
- applet = _applet;
- }
-
- public void run()
- {
- LoadJmolThread jmolchecker = new LoadJmolThread();
- jmolchecker.start();
- while (jmolchecker.notFinished())
- {
- // wait around until the Jmol check is complete.
- try
- {
- Thread.sleep(2);
- } catch (Exception e)
- {
- }
- ;
- }
- startLoading();
- // applet.callInitCallback();
- }
-
- private void startLoading()
- {
- AlignFrame newAlignFrame;
- dbgMsg("Loading thread started with:\n>>file\n" + _file + ">>endfile");
- file = setProtocolState(_file);
-
- format = new jalview.io.IdentifyFile().Identify(file, protocol);
- dbgMsg("File identified as '" + format + "'");
- dbgMsg("Loading started.");
- Alignment al = null;
- try
- {
- al = new AppletFormatAdapter().readFile(file, protocol, format);
- } catch (java.io.IOException ex)
- {
- dbgMsg("File load exception.");
- ex.printStackTrace();
- if (debug)
- {
- try
- {
- FileParse fp = new FileParse(file, protocol);
- String ln = 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.");
- e.printStackTrace();
- }
- }
- }
- if ((al != null) && (al.getHeight() > 0))
- {
- dbgMsg("Successfully loaded file.");
- newAlignFrame = new AlignFrame(al, applet, file, embedded);
- if (initialAlignFrame == null)
- {
- initialAlignFrame = newAlignFrame;
- }
- // update the focus.
- currentAlignFrame = newAlignFrame;
-
- if (protocol == jalview.io.AppletFormatAdapter.PASTE)
- {
- newAlignFrame.setTitle("Sequences from "
- + applet.getDocumentBase());
- }
-
- newAlignFrame.statusBar.setText("Successfully loaded file " + file);
-
- String treeFile = applet.getParameter("tree");
- if (treeFile == null)
- {
- treeFile = applet.getParameter("treeFile");
- }
-
- if (treeFile != null)
- {
- try
- {
- treeFile = setProtocolState(treeFile);
- /*
- * if (inArchive(treeFile)) { protocol =
- * AppletFormatAdapter.CLASSLOADER; } else { protocol =
- * AppletFormatAdapter.URL; treeFile = addProtocol(treeFile); }
- */
- jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile,
- protocol);
-
- fin.parse();
-
- if (fin.getTree() != null)
- {
- newAlignFrame.loadTree(fin, treeFile);
- dbgMsg("Successfuly imported tree.");
- }
- else
- {
- dbgMsg("Tree parameter did not resolve to a valid tree.");
- }
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
- String param = applet.getParameter("features");
- if (param != null)
- {
- param = setProtocolState(param);
-
- newAlignFrame.parseFeaturesFile(param, protocol);
- }
-
- param = applet.getParameter("showFeatureSettings");
- if (param != null && param.equalsIgnoreCase("true"))
- {
- newAlignFrame.viewport.showSequenceFeatures(true);
- new FeatureSettings(newAlignFrame.alignPanel);
- }
-
- param = applet.getParameter("annotations");
- if (param != null)
- {
- param = setProtocolState(param);
-
- if (new AnnotationFile().readAnnotationFile(
- newAlignFrame.viewport.getAlignment(), param, protocol))
- {
- newAlignFrame.alignPanel.fontChanged();
- newAlignFrame.alignPanel.setScrollValues(0, 0);
- }
- else
- {
- System.err
- .println("Annotations were not added from annotation file '"
- + param + "'");
- }
-
- }
-
- param = applet.getParameter("jnetfile");
- if (param != null)
- {
- try
- {
- param = setProtocolState(param);
- jalview.io.JPredFile predictions = new jalview.io.JPredFile(
- param, protocol);
- JnetAnnotationMaker.add_annotation(predictions,
- newAlignFrame.viewport.getAlignment(), 0, false); // false==do
- // not
- // add
- // sequence
- // profile
- // from
- // concise
- // output
- newAlignFrame.alignPanel.fontChanged();
- newAlignFrame.alignPanel.setScrollValues(0, 0);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
- /*
- * Undocumented for 2.6
- * - related to JAL-434
- */
- applet.setAlignPdbStructures(getDefaultParameter("alignpdbfiles",
- false));
- /*
- *
- *
- *
- *
- *
- */
-
- 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 = applet.getParameter("PDBFILE" + pdbFileCount);
- else
- param = applet.getParameter("PDBFILE");
-
- if (param != null)
- {
- PDBEntry pdb = new PDBEntry();
-
- String seqstring;
- SequenceI[] seqs = null;
- String[] chains = null;
-
- StringTokenizer st = new StringTokenizer(param, " ");
-
- if (st.countTokens() < 2)
- {
- String sequence = applet.getParameter("PDBSEQ");
- if (sequence != null)
- seqs = new SequenceI[]
- { (Sequence) newAlignFrame.getAlignViewport()
- .getAlignment().findName(sequence) };
-
- }
- else
- {
- param = st.nextToken();
- Vector tmp = new Vector();
- Vector tmp2 = new Vector();
-
- while (st.hasMoreTokens())
- {
- seqstring = st.nextToken();
- StringTokenizer st2 = new StringTokenizer(seqstring, "=");
- if (st2.countTokens() > 1)
- {
- // This is the chain
- tmp2.addElement(st2.nextToken());
- seqstring = st2.nextToken();
- }
- tmp.addElement((Sequence) newAlignFrame.getAlignViewport()
- .getAlignment().findName(seqstring));
- }
-
- seqs = new SequenceI[tmp.size()];
- tmp.copyInto(seqs);
- if (tmp2.size() == tmp.size())
- {
- chains = new String[tmp2.size()];
- tmp2.copyInto(chains);
- }
- }
- param = setProtocolState(param);
-
- if (// !jmolAvailable
- // &&
- protocol == AppletFormatAdapter.CLASSLOADER)
- {
- // TODO: verify this Re:
- // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
- // This exception preserves the current behaviour where, even if
- // the local pdb file was identified in the class loader
- protocol = AppletFormatAdapter.URL; // this is probably NOT
- // CORRECT!
- param = addProtocol(param); //
- }
-
- pdb.setFile(param);
-
- if (seqs != null)
- {
- for (int i = 0; i < seqs.length; i++)
- {
- if (seqs[i] != null)
- {
- ((Sequence) seqs[i]).addPDBId(pdb);
- }
- else
- {
- if (JalviewLite.debug)
- {
- // this may not really be a problem but we give a warning
- // anyway
- System.err
- .println("Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "
- + i + ")");
- }
- }
- }
-
- 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 = applet.getParameter("hidefeaturegroups");
- if (param != null)
- {
- applet.setFeatureGroupStateOn(newAlignFrame, param, false);
- }
- // show specific groups
- param = applet.getParameter("showfeaturegroups");
- if (param != null)
- {
- applet.setFeatureGroupStateOn(newAlignFrame, param, true);
- }
- }
- else
- {
- fileFound = false;
- applet.remove(launcher);
- applet.repaint();
- }
- }
-
- /**
- * Discovers whether the given file is in the Applet Archive
- *
- * @param file
- * String
- * @return boolean
- */
- boolean inArchive(String file)
- {
- // This might throw a security exception in certain browsers
- // Netscape Communicator for instance.
- try
- {
- boolean rtn = (getClass().getResourceAsStream("/" + file) != null);
- if (debug)
- {
- System.err.println("Resource '" + file + "' was "
- + (rtn ? "" : "not") + " located by classloader.");
- }
- return rtn;
- } catch (Exception ex)
- {
- System.out.println("Exception checking resources: " + file + " "
- + ex);
- return false;
- }
- }
-
- String addProtocol(String file)
- {
- if (file.indexOf("://") == -1)
- {
- file = applet.getCodeBase() + file;
- if (debug)
- {
- System.err.println("Prepended codebase for resource: '" + file
- + "'");
- }
- }
-
- return file;
- }
- }
-
- /**
- * @return the default alignFrame acted on by the public applet methods. May
- * return null with an error message on System.err indicating the
- * fact.
- */
- public AlignFrame getDefaultTargetFrame()
- {
- if (currentAlignFrame != null)
- {
- return currentAlignFrame;
- }
- if (initialAlignFrame != null)
- {
- return initialAlignFrame;
- }
- System.err
- .println("Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");
- return null;
- }
-
- /**
- * separator used for separatorList
- */
- protected String separator = ""+((char)0x00AC); // the default used to be '|' but many sequence IDS include pipes.
-
- /**
- * parse the string into a list
- *
- * @param list
- * @return elements separated by separator
- */
- 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("") || list.equals(separator))
- return null;
- java.util.Vector jv = new Vector();
- int cp = 0, pos;
- while ((pos = list.indexOf(separator, cp)) > cp)
- {
- jv.addElement(list.substring(cp, pos));
- cp = pos + seplen;
- }
- if (cp < list.length())
- {
- String c = list.substring(cp);
- if (!c.equals(separator))
- {
- jv.addElement(c);
- }
- }
- if (jv.size() > 0)
- {
- String[] v = new String[jv.size()];
- for (int i = 0; i < v.length; i++)
- {
- v[i] = (String) jv.elementAt(i);
- }
- jv.removeAllElements();
- if (debug)
- {
- System.err.println("Array from '" + separator
- + "' separated List:\n" + v.length);
- for (int i = 0; i < v.length; i++)
- {
- System.err.println("item " + i + " '" + v[i] + "'");
- }
- }
- return v;
- }
- if (debug)
- {
- System.err.println("Empty Array from '" + separator
- + "' separated List");
- }
- return null;
- }
-
- /**
- * concatenate the list with separator
- *
- * @param list
- * @return concatenated string
- */
- 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 && list.length > 0)
- {
- for (int i = 0, iSize = list.length; i < iSize; i++)
- {
- if (list[i] != null)
- {
- if (i > 0)
- {
- v.append(separator);
- }
- v.append(list[i]);
- }
- }
- if (debug)
- {
- System.err.println("Returning '" + separator
- + "' separated List:\n");
- System.err.println(v);
- }
- return v.toString();
- }
- if (debug)
- {
- System.err.println("Returning empty '" + separator
- + "' separated List\n");
- }
- return "" + separator;
- }
-
- /**
- * @return
- * @see jalview.appletgui.AlignFrame#getFeatureGroups()
- */
- public String getFeatureGroups()
- {
- String lst = arrayToSeparatorList(getDefaultTargetFrame()
- .getFeatureGroups());
- return lst;
- }
-
- /**
- * @param alf
- * alignframe to get feature groups on
- * @return
- * @see jalview.appletgui.AlignFrame#getFeatureGroups()
- */
- public String getFeatureGroupsOn(AlignFrame alf)
- {
- String lst = arrayToSeparatorList(alf.getFeatureGroups());
- return lst;
- }
-
- /**
- * @param visible
- * @return
- * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)
- */
- public String getFeatureGroupsOfState(boolean visible)
- {
- return arrayToSeparatorList(getDefaultTargetFrame()
- .getFeatureGroupsOfState(visible));
- }
-
- /**
- * @param alf
- * align frame to get groups of state visible
- * @param visible
- * @return
- * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)
- */
- public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
- {
- return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));
- }
-
- /**
- * @param groups
- * tab separated list of group names
- * @param state
- * true or false
- * @see jalview.appletgui.AlignFrame#setFeatureGroupState(java.lang.String[],
- * boolean)
- */
- public void setFeatureGroupStateOn(AlignFrame alf, String groups,
- boolean state)
- {
- boolean st = state;// !(state==null || state.equals("") ||
- // state.toLowerCase().equals("false"));
- alf.setFeatureGroupState(separatorListToArray(groups), st);
- }
-
- public void setFeatureGroupState(String groups, boolean state)
- {
- setFeatureGroupStateOn(getDefaultTargetFrame(), groups, state);
- }
-
- /**
- * List separator string
- *
- * @return the separator
- */
- public String getSeparator()
- {
- return separator;
- }
-
- /**
- * List separator string
- *
- * @param separator
- * 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; }
- */
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * 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.
+ *
+ * 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 .
+ */
+package jalview.bin;
+
+import jalview.api.StructureSelectionManagerProvider;
+import jalview.appletgui.AlignFrame;
+import jalview.appletgui.AlignViewport;
+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.JalviewLiteJsApi;
+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.EventQueue;
+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.net.URL;
+import java.util.Hashtable;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import netscape.javascript.JSObject;
+
+/**
+ * Jalview Applet. Runs in Java 1.18 runtime
+ *
+ * @author $author$
+ * @version $Revision: 1.92 $
+ */
+public class JalviewLite extends Applet implements
+ StructureSelectionManagerProvider, JalviewLiteJsApi
+{
+
+ public StructureSelectionManager getStructureSelectionManager()
+ {
+ return StructureSelectionManager.getStructureSelectionManager(this);
+ }
+
+ // /////////////////////////////////////////
+ // The following public methods maybe called
+ // externally, eg via javascript in HTML page
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences()
+ */
+ public String getSelectedSequences()
+ {
+ return getSelectedSequencesFrom(getDefaultTargetFrame());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences(java.lang.String)
+ */
+ public String getSelectedSequences(String sep)
+ {
+ return getSelectedSequencesFrom(getDefaultTargetFrame(), sep);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
+ * .AlignFrame)
+ */
+ public String getSelectedSequencesFrom(AlignFrame alf)
+ {
+ return getSelectedSequencesFrom(alf, separator); // ""+0x00AC);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
+ * .AlignFrame, java.lang.String)
+ */
+ public String getSelectedSequencesFrom(AlignFrame alf, String sep)
+ {
+ StringBuffer result = new StringBuffer("");
+ if (sep == null || sep.length() == 0)
+ {
+ sep = separator; // "+0x00AC;
+ }
+ if (alf.viewport.getSelectionGroup() != null)
+ {
+ SequenceI[] seqs = alf.viewport.getSelectionGroup()
+ .getSequencesInOrder(alf.viewport.getAlignment());
+
+ for (int i = 0; i < seqs.length; i++)
+ {
+ result.append(seqs[i].getName());
+ result.append(sep);
+ }
+ }
+
+ return result.toString();
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#highlight(java.lang.String,
+ * java.lang.String, java.lang.String)
+ */
+ public void highlight(String sequenceId, String position,
+ String alignedPosition)
+ {
+ highlightIn(getDefaultTargetFrame(), sequenceId, position,
+ alignedPosition);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#highlightIn(jalview.appletgui.AlignFrame,
+ * java.lang.String, java.lang.String, java.lang.String)
+ */
+ public void highlightIn(final AlignFrame alf, final String sequenceId,
+ final String position, final 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());
+ final SequenceI sq = matcher.findIdMatch(sequenceId);
+ if (sq != null)
+ {
+ int apos = -1;
+ try
+ {
+ apos = new Integer(position).intValue();
+ apos--;
+ } catch (NumberFormatException ex)
+ {
+ return;
+ }
+ final StructureSelectionManagerProvider me = this;
+ final int pos = apos;
+ // use vamsas listener to broadcast to all listeners in scope
+ if (alignedPosition != null
+ && (alignedPosition.trim().length() == 0 || alignedPosition
+ .toLowerCase().indexOf("false") > -1))
+ {
+ java.awt.EventQueue.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ StructureSelectionManager.getStructureSelectionManager(me)
+ .mouseOverVamsasSequence(sq, sq.findIndex(pos), null);
+ }
+ });
+ }
+ else
+ {
+ java.awt.EventQueue.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ StructureSelectionManager.getStructureSelectionManager(me)
+ .mouseOverVamsasSequence(sq, pos, null);
+ }
+ });
+ }
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#select(java.lang.String,
+ * java.lang.String)
+ */
+ public void select(String sequenceIds, String columns)
+ {
+ selectIn(getDefaultTargetFrame(), sequenceIds, columns, separator);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#select(java.lang.String,
+ * java.lang.String, java.lang.String)
+ */
+ public void select(String sequenceIds, String columns, String sep)
+ {
+ selectIn(getDefaultTargetFrame(), sequenceIds, columns, sep);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame,
+ * java.lang.String, java.lang.String)
+ */
+ public void selectIn(AlignFrame alf, String sequenceIds, String columns)
+ {
+ selectIn(alf, sequenceIds, columns, separator);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame,
+ * java.lang.String, java.lang.String, java.lang.String)
+ */
+ public void selectIn(final 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);
+ final SequenceGroup sel = new SequenceGroup();
+ final 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);
+ EventQueue.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ alf.select(sel, csel);
+ }
+ });
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignment(java.lang.
+ * String, java.lang.String)
+ */
+ public String getSelectedSequencesAsAlignment(String format, String suffix)
+ {
+ return getSelectedSequencesAsAlignmentFrom(getDefaultTargetFrame(),
+ format, suffix);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignmentFrom(jalview
+ * .appletgui.AlignFrame, java.lang.String, java.lang.String)
+ */
+ public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
+ String format, String suffix)
+ {
+ try
+ {
+ boolean seqlimits = suffix.equalsIgnoreCase("true");
+ if (alf.viewport.getSelectionGroup() != null)
+ {
+ String reply = new AppletFormatAdapter().formatSequences(format,
+ new Alignment(alf.viewport.getSelectionAsNewSequence()),
+ seqlimits);
+ return reply;
+ }
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ return "Error retrieving alignment in " + format + " format. ";
+ }
+ return "";
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getAlignmentOrder()
+ */
+ public String getAlignmentOrder()
+ {
+ return getAlignmentOrderFrom(getDefaultTargetFrame());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame
+ * )
+ */
+ public String getAlignmentOrderFrom(AlignFrame alf)
+ {
+ return getAlignmentOrderFrom(alf, separator);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame
+ * , java.lang.String)
+ */
+ 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);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String,
+ * java.lang.String)
+ */
+ public String orderBy(String order, String undoName)
+ {
+ return orderBy(order, undoName, separator);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String,
+ * java.lang.String, java.lang.String)
+ */
+ public String orderBy(String order, String undoName, String sep)
+ {
+ return orderAlignmentBy(getDefaultTargetFrame(), order, undoName, sep);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#orderAlignmentBy(jalview.appletgui.AlignFrame,
+ * java.lang.String, java.lang.String, java.lang.String)
+ */
+ 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 "";
+ }
+ ;
+ final AlignmentOrder aorder = new AlignmentOrder(sqs);
+
+ if (undoName != null && undoName.trim().length() == 0)
+ {
+ undoName = null;
+ }
+ final String _undoName = undoName;
+ // TODO: deal with synchronization here: cannot raise any events until after
+ // this has returned.
+ return alf.sortBy(aorder, _undoName) ? "true" : "";
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String)
+ */
+ public String getAlignment(String format)
+ {
+ return getAlignmentFrom(getDefaultTargetFrame(), format, "true");
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,
+ * java.lang.String)
+ */
+ public String getAlignmentFrom(AlignFrame alf, String format)
+ {
+ return getAlignmentFrom(alf, format, "true");
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String,
+ * java.lang.String)
+ */
+ public String getAlignment(String format, String suffix)
+ {
+ return getAlignmentFrom(getDefaultTargetFrame(), format, suffix);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,
+ * java.lang.String, java.lang.String)
+ */
+ public String getAlignmentFrom(AlignFrame alf, String format,
+ String suffix)
+ {
+ try
+ {
+ boolean seqlimits = suffix.equalsIgnoreCase("true");
+
+ String reply = new AppletFormatAdapter().formatSequences(format,
+ alf.viewport.getAlignment(), seqlimits);
+ return reply;
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ return "Error retrieving alignment in " + format + " format. ";
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)
+ */
+ public void loadAnnotation(String annotation)
+ {
+ loadAnnotationFrom(getDefaultTargetFrame(), annotation);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame
+ * , java.lang.String)
+ */
+ public void loadAnnotationFrom(AlignFrame alf, String annotation)
+ {
+ if (new AnnotationFile().readAnnotationFile(alf.getAlignViewport()
+ .getAlignment(), annotation, AppletFormatAdapter.PASTE))
+ {
+ alf.alignPanel.fontChanged();
+ alf.alignPanel.setScrollValues(0, 0);
+ }
+ else
+ {
+ alf.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE);
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getFeatures(java.lang.String)
+ */
+ public String getFeatures(String format)
+ {
+ return getFeaturesFrom(getDefaultTargetFrame(), format);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getFeaturesFrom(jalview.appletgui.AlignFrame,
+ * java.lang.String)
+ */
+ public String getFeaturesFrom(AlignFrame alf, String format)
+ {
+ return alf.outputFeatures(false, format);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getAnnotation()
+ */
+ public String getAnnotation()
+ {
+ return getAnnotationFrom(getDefaultTargetFrame());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getAnnotationFrom(jalview.appletgui.AlignFrame
+ * )
+ */
+ public String getAnnotationFrom(AlignFrame alf)
+ {
+ return alf.outputAnnotations(false);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#newView()
+ */
+ public AlignFrame newView()
+ {
+ return newViewFrom(getDefaultTargetFrame());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#newView(java.lang.String)
+ */
+ public AlignFrame newView(String name)
+ {
+ return newViewFrom(getDefaultTargetFrame(), name);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame)
+ */
+ public AlignFrame newViewFrom(AlignFrame alf)
+ {
+ return alf.newView(null);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame,
+ * java.lang.String)
+ */
+ public AlignFrame newViewFrom(AlignFrame alf, String name)
+ {
+ return alf.newView(name);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#loadAlignment(java.lang.String,
+ * java.lang.String)
+ */
+ public AlignFrame loadAlignment(String text, String title)
+ {
+ Alignment al = null;
+
+ String format = new IdentifyFile().Identify(text,
+ AppletFormatAdapter.PASTE);
+ try
+ {
+ al = new AppletFormatAdapter().readFile(text,
+ AppletFormatAdapter.PASTE, format);
+ if (al.getHeight() > 0)
+ {
+ return new AlignFrame(al, this, title, false);
+ }
+ } catch (java.io.IOException ex)
+ {
+ ex.printStackTrace();
+ }
+ return null;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#setMouseoverListener(java.lang.String)
+ */
+ public void setMouseoverListener(String listener)
+ {
+ setMouseoverListener(currentAlignFrame, listener);
+ }
+
+ private Vector javascriptListeners = new Vector();
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#setMouseoverListener(jalview.appletgui.AlignFrame
+ * , java.lang.String)
+ */
+ 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(this)
+ .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.");
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#setSelectionListener(java.lang.String)
+ */
+ public void setSelectionListener(String listener)
+ {
+ setSelectionListener(null, listener);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#setSelectionListener(jalview.appletgui.AlignFrame
+ * , java.lang.String)
+ */
+ 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(this)
+ .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.");
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#setStructureListener(java.lang.String,
+ * java.lang.String)
+ */
+ public void setStructureListener(String listener, String modelSet)
+ {
+ 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, separatorListToArray(modelSet));
+ javascriptListeners.addElement(mol);
+ StructureSelectionManager.getStructureSelectionManager(this)
+ .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.");
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#removeJavascriptListener(jalview.appletgui
+ * .AlignFrame, java.lang.String)
+ */
+ 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(this)
+ .removeSelectionListener((SelectionListener) lstner);
+ }
+ else
+ {
+ StructureSelectionManager.getStructureSelectionManager(this)
+ .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()
+ {
+ System.err.println("Applet " + getName() + " stop().");
+ tidyUp();
+ }
+
+ public void destroy()
+ {
+ System.err.println("Applet " + getName() + " destroy().");
+ tidyUp();
+ }
+
+ private void tidyUp()
+ {
+ removeAll();
+ if (currentAlignFrame != null && currentAlignFrame.viewport != null
+ && currentAlignFrame.viewport.applet != null)
+ {
+ AlignViewport av = currentAlignFrame.viewport;
+ currentAlignFrame.closeMenuItem_actionPerformed();
+ av.applet = null;
+ currentAlignFrame = null;
+ }
+ if (javascriptListeners != null)
+ {
+ while (javascriptListeners.size() > 0)
+ {
+ jalview.javascript.JSFunctionExec mol = javascriptListeners
+ .elementAt(0);
+ javascriptListeners.removeElement(mol);
+ if (mol instanceof SelectionListener)
+ {
+ StructureSelectionManager.getStructureSelectionManager(this)
+ .removeSelectionListener((SelectionListener) mol);
+ }
+ else
+ {
+ StructureSelectionManager.getStructureSelectionManager(this)
+ .removeStructureViewerListener(mol, null);
+ }
+ mol.jvlite = null;
+ }
+ }
+ if (jsFunctionExec != null)
+ {
+ jsFunctionExec.stopQueue();
+ jsFunctionExec.jvlite = null;
+ }
+ initialAlignFrame = null;
+ jsFunctionExec = null;
+ javascriptListeners = null;
+ StructureSelectionManager.release(this);
+ }
+
+ private jalview.javascript.JSFunctionExec jsFunctionExec;
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#mouseOverStructure(java.lang.String,
+ * java.lang.String, java.lang.String)
+ */
+ public void mouseOverStructure(final String pdbResNum,
+ final String chain, final String pdbfile)
+ {
+ final StructureSelectionManagerProvider me = this;
+ java.awt.EventQueue.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ try
+ {
+ StructureSelectionManager.getStructureSelectionManager(me)
+ .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 + "'");
+ }
+
+ }
+ });
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#scrollViewToIn(jalview.appletgui.AlignFrame,
+ * java.lang.String, java.lang.String)
+ */
+ public void scrollViewToIn(final AlignFrame alf, final String topRow,
+ final String leftHandColumn)
+ {
+ java.awt.EventQueue.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ try
+ {
+ alf.scrollTo(new Integer(topRow).intValue(), new Integer(
+ leftHandColumn).intValue());
+
+ } catch (Exception ex)
+ {
+ System.err.println("Couldn't parse integer arguments (topRow='"
+ + topRow + "' and leftHandColumn='" + leftHandColumn
+ + "')");
+ ex.printStackTrace();
+ }
+ }
+ });
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.javascript.JalviewLiteJsApi#scrollViewToRowIn(jalview.appletgui
+ * .AlignFrame, java.lang.String)
+ */
+ @Override
+ public void scrollViewToRowIn(final AlignFrame alf, final String topRow)
+ {
+
+ java.awt.EventQueue.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ try
+ {
+ alf.scrollToRow(new Integer(topRow).intValue());
+
+ } catch (Exception ex)
+ {
+ System.err.println("Couldn't parse integer arguments (topRow='"
+ + topRow + "')");
+ ex.printStackTrace();
+ }
+
+ }
+ });
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.javascript.JalviewLiteJsApi#scrollViewToColumnIn(jalview.appletgui
+ * .AlignFrame, java.lang.String)
+ */
+ @Override
+ public void scrollViewToColumnIn(final AlignFrame alf,
+ final String leftHandColumn)
+ {
+ java.awt.EventQueue.invokeLater(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ try
+ {
+ alf.scrollToColumn(new Integer(leftHandColumn).intValue());
+
+ } catch (Exception ex)
+ {
+ System.err
+ .println("Couldn't parse integer arguments (leftHandColumn='"
+ + leftHandColumn + "')");
+ ex.printStackTrace();
+ }
+ }
+ });
+
+ }
+
+ // //////////////////////////////////////////////
+ // //////////////////////////////////////////////
+
+ public static int lastFrameX = 200;
+
+ public static int lastFrameY = 200;
+
+ boolean fileFound = true;
+
+ String file = "No file";
+
+ Button launcher = new Button("Start Jalview");
+
+ /**
+ * The currentAlignFrame is static, it will change if and when the user
+ * selects a new window. Note that it will *never* point back to the embedded
+ * AlignFrame if the applet is started as embedded on the page and then
+ * afterwards a new view is created.
+ */
+ 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;
+
+ 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
+
+ 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;
+
+ 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
+ */
+ String dbg = getParameter("debug");
+ if (dbg != null)
+ {
+ debug = dbg.toLowerCase().equals("true");
+ }
+ if (debug)
+ {
+
+ System.err.println("JalviewLite Version " + getVersion());
+ 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
+ */
+ String chkforJmol = getParameter("nojmol");
+ if (chkforJmol != null)
+ {
+ checkForJmol = !chkforJmol.equals("true");
+ }
+ /**
+ * get the separator parameter if present
+ */
+ String sep = getParameter("separator");
+ if (sep != null)
+ {
+ if (sep.length() > 0)
+ {
+ separator = sep;
+ if (debug)
+ {
+ System.err.println("Separator set to '" + separator + "'");
+ }
+ }
+ else
+ {
+ throw new Error(
+ "Invalid separator parameter - must be non-zero length");
+ }
+ }
+ int r = 255;
+ int g = 255;
+ int b = 255;
+ String param = getParameter("RGB");
+
+ if (param != null)
+ {
+ try
+ {
+ r = Integer.parseInt(param.substring(0, 2), 16);
+ g = Integer.parseInt(param.substring(2, 4), 16);
+ b = Integer.parseInt(param.substring(4, 6), 16);
+ } catch (Exception ex)
+ {
+ r = 255;
+ g = 255;
+ b = 255;
+ }
+ }
+ param = getParameter("label");
+ if (param != null)
+ {
+ launcher.setLabel(param);
+ }
+
+ setBackground(new Color(r, g, b));
+
+ file = getParameter("file");
+
+ if (file == null)
+ {
+ // Maybe the sequences are added as parameters
+ StringBuffer data = new StringBuffer("PASTE");
+ int i = 1;
+ while ((file = getParameter("sequence" + i)) != null)
+ {
+ data.append(file.toString() + "\n");
+ i++;
+ }
+ if (data.length() > 5)
+ {
+ file = data.toString();
+ }
+ }
+
+ 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, jvapplet);
+ loader.start();
+ }
+ else if (file != null)
+ {
+ if (getParameter("showbutton") == null
+ || !getParameter("showbutton").equalsIgnoreCase("false"))
+ {
+ // Add the JalviewLite 'Button' to the page
+ add(launcher);
+ launcher.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ LoadingThread loader = new LoadingThread(file, jvapplet);
+ loader.start();
+ }
+ });
+ }
+ else
+ {
+ // Open jalviewLite immediately.
+ LoadingThread loader = new LoadingThread(file, jvapplet);
+ loader.start();
+ }
+ }
+ else
+ {
+ // jalview initialisation with no alignment. loadAlignment() method can
+ // 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
+ * @param title
+ * title of new frame
+ * @param width
+ * width if new frame
+ * @param height
+ * height of new frame
+ */
+ public static void addFrame(final Frame frame, String title, int width,
+ int height)
+ {
+ frame.setLocation(lastFrameX, lastFrameY);
+ lastFrameX += 40;
+ lastFrameY += 40;
+ frame.setSize(width, height);
+ frame.setTitle(title);
+ frame.addWindowListener(new WindowAdapter()
+ {
+ public void windowClosing(WindowEvent e)
+ {
+ if (frame instanceof AlignFrame)
+ {
+ AlignViewport vp = ((AlignFrame) frame).viewport;
+ ((AlignFrame) frame).closeMenuItem_actionPerformed();
+ if (vp.applet.currentAlignFrame == frame)
+ {
+ vp.applet.currentAlignFrame = null;
+ }
+ vp.applet = null;
+ vp = null;
+
+ }
+ lastFrameX -= 40;
+ lastFrameY -= 40;
+ if (frame instanceof EmbmenuFrame)
+ {
+ ((EmbmenuFrame) frame).destroyMenus();
+ }
+ frame.setMenuBar(null);
+ frame.dispose();
+ }
+
+ public void windowActivated(WindowEvent e)
+ {
+ if (frame instanceof AlignFrame)
+ {
+ ((AlignFrame) frame).viewport.applet.currentAlignFrame = (AlignFrame) frame;
+ if (debug)
+ {
+ System.err.println("Activated window " + frame);
+ }
+ }
+ // be good.
+ super.windowActivated(e);
+ }
+ /*
+ * Probably not necessary to do this - see TODO above. (non-Javadoc)
+ *
+ * @see
+ * java.awt.event.WindowAdapter#windowDeactivated(java.awt.event.WindowEvent
+ * )
+ *
+ * public void windowDeactivated(WindowEvent e) { if (currentAlignFrame ==
+ * frame) { currentAlignFrame = null; if (debug) {
+ * System.err.println("Deactivated window "+frame); } }
+ * super.windowDeactivated(e); }
+ */
+ });
+ frame.setVisible(true);
+ }
+
+ /**
+ * This paints the background surrounding the "Launch Jalview button"
+ *
+ * If file given in parameter not found, displays error message
+ *
+ * @param g
+ * graphics context
+ */
+ public void paint(Graphics g)
+ {
+ if (!fileFound)
+ {
+ g.setColor(new Color(200, 200, 200));
+ g.setColor(Color.cyan);
+ g.fillRect(0, 0, getSize().width, getSize().height);
+ g.setColor(Color.red);
+ g.drawString("Jalview can't open file", 5, 15);
+ g.drawString("\"" + file + "\"", 5, 30);
+ }
+ else if (embedded)
+ {
+ g.setColor(Color.black);
+ g.setFont(new Font("Arial", Font.BOLD, 24));
+ 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;
+
+ public void run()
+ {
+ if (running || checkedForJmol)
+ {
+ return;
+ }
+ running = true;
+ if (checkForJmol)
+ {
+ try
+ {
+ if (!System.getProperty("java.version").startsWith("1.1"))
+ {
+ Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter");
+ jmolAvailable = true;
+ }
+ if (!jmolAvailable)
+ {
+ System.out
+ .println("Jmol not available - Using MCview for structures");
+ }
+ } catch (java.lang.ClassNotFoundException ex)
+ {
+ }
+ }
+ else
+ {
+ jmolAvailable = false;
+ if (debug)
+ {
+ System.err
+ .println("Skipping Jmol check. Will use MCView (probably)");
+ }
+ }
+ checkedForJmol = true;
+ running = false;
+ }
+
+ public boolean notFinished()
+ {
+ return running || !checkedForJmol;
+ }
+ }
+
+ class LoadingThread extends Thread
+ {
+ /**
+ * State variable: File source
+ */
+ String file;
+
+ /**
+ * State variable: protocol for access to file source
+ */
+ String protocol;
+
+ /**
+ * State variable: format of file source
+ */
+ String format;
+
+ String _file;
+
+ JalviewLite applet;
+
+ private void dbgMsg(String msg)
+ {
+ if (applet.debug)
+ {
+ System.err.println(msg);
+ }
+ }
+
+ /**
+ * update the protocol state variable for accessing the datasource located
+ * by file.
+ *
+ * @param file
+ * @return possibly updated datasource string
+ */
+ public String setProtocolState(String file)
+ {
+ if (file.startsWith("PASTE"))
+ {
+ file = file.substring(5);
+ protocol = AppletFormatAdapter.PASTE;
+ }
+ else if (inArchive(file))
+ {
+ protocol = AppletFormatAdapter.CLASSLOADER;
+ }
+ else
+ {
+ file = addProtocol(file);
+ protocol = AppletFormatAdapter.URL;
+ }
+ dbgMsg("Protocol identified as '" + protocol + "'");
+ return file;
+ }
+
+ public LoadingThread(String _file, JalviewLite _applet)
+ {
+ this._file = _file;
+ applet = _applet;
+ }
+
+ public void run()
+ {
+ LoadJmolThread jmolchecker = new LoadJmolThread();
+ jmolchecker.start();
+ while (jmolchecker.notFinished())
+ {
+ // wait around until the Jmol check is complete.
+ try
+ {
+ Thread.sleep(2);
+ } catch (Exception e)
+ {
+ }
+ ;
+ }
+ startLoading();
+ // applet.callInitCallback();
+ }
+
+ private void startLoading()
+ {
+ AlignFrame newAlignFrame;
+ dbgMsg("Loading thread started with:\n>>file\n" + _file + ">>endfile");
+ file = setProtocolState(_file);
+
+ format = new jalview.io.IdentifyFile().Identify(file, protocol);
+ dbgMsg("File identified as '" + format + "'");
+ dbgMsg("Loading started.");
+ Alignment al = null;
+ try
+ {
+ al = new AppletFormatAdapter().readFile(file, protocol, format);
+ } catch (java.io.IOException ex)
+ {
+ dbgMsg("File load exception.");
+ ex.printStackTrace();
+ if (debug)
+ {
+ try
+ {
+ FileParse fp = new FileParse(file, protocol);
+ String ln = 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.");
+ e.printStackTrace();
+ }
+ }
+ }
+ if ((al != null) && (al.getHeight() > 0))
+ {
+ dbgMsg("Successfully loaded file.");
+ newAlignFrame = new AlignFrame(al, applet, file, embedded);
+ if (initialAlignFrame == null)
+ {
+ initialAlignFrame = newAlignFrame;
+ }
+ // update the focus.
+ currentAlignFrame = newAlignFrame;
+
+ if (protocol == jalview.io.AppletFormatAdapter.PASTE)
+ {
+ newAlignFrame.setTitle("Sequences from "
+ + applet.getDocumentBase());
+ }
+
+ newAlignFrame.statusBar.setText("Successfully loaded file " + file);
+
+ String treeFile = applet.getParameter("tree");
+ if (treeFile == null)
+ {
+ treeFile = applet.getParameter("treeFile");
+ }
+
+ if (treeFile != null)
+ {
+ try
+ {
+ treeFile = setProtocolState(treeFile);
+ /*
+ * if (inArchive(treeFile)) { protocol =
+ * AppletFormatAdapter.CLASSLOADER; } else { protocol =
+ * AppletFormatAdapter.URL; treeFile = addProtocol(treeFile); }
+ */
+ jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile,
+ protocol);
+
+ fin.parse();
+
+ if (fin.getTree() != null)
+ {
+ newAlignFrame.loadTree(fin, treeFile);
+ dbgMsg("Successfuly imported tree.");
+ }
+ else
+ {
+ dbgMsg("Tree parameter did not resolve to a valid tree.");
+ }
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ String param = applet.getParameter("features");
+ if (param != null)
+ {
+ param = setProtocolState(param);
+
+ newAlignFrame.parseFeaturesFile(param, protocol);
+ }
+
+ param = applet.getParameter("showFeatureSettings");
+ if (param != null && param.equalsIgnoreCase("true"))
+ {
+ newAlignFrame.viewport.showSequenceFeatures(true);
+ new FeatureSettings(newAlignFrame.alignPanel);
+ }
+
+ param = applet.getParameter("annotations");
+ if (param != null)
+ {
+ param = setProtocolState(param);
+
+ if (new AnnotationFile().readAnnotationFile(
+ newAlignFrame.viewport.getAlignment(), param, protocol))
+ {
+ newAlignFrame.alignPanel.fontChanged();
+ newAlignFrame.alignPanel.setScrollValues(0, 0);
+ }
+ else
+ {
+ System.err
+ .println("Annotations were not added from annotation file '"
+ + param + "'");
+ }
+
+ }
+
+ param = applet.getParameter("jnetfile");
+ if (param != null)
+ {
+ try
+ {
+ param = setProtocolState(param);
+ jalview.io.JPredFile predictions = new jalview.io.JPredFile(
+ param, protocol);
+ JnetAnnotationMaker.add_annotation(predictions,
+ newAlignFrame.viewport.getAlignment(), 0, false); // false==do
+ // not
+ // add
+ // sequence
+ // profile
+ // from
+ // concise
+ // output
+ newAlignFrame.alignPanel.fontChanged();
+ newAlignFrame.alignPanel.setScrollValues(0, 0);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ /*
+ * Undocumented for 2.6
+ * - related to JAL-434
+ */
+ applet.setAlignPdbStructures(getDefaultParameter("alignpdbfiles",
+ false));
+ /*
+ *
+ *
+ *
+ *
+ *
+ */
+
+ 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 = applet.getParameter("PDBFILE" + pdbFileCount);
+ }
+ else
+ {
+ param = applet.getParameter("PDBFILE");
+ }
+
+ if (param != null)
+ {
+ PDBEntry pdb = new PDBEntry();
+
+ String seqstring;
+ SequenceI[] seqs = null;
+ String[] chains = null;
+
+ StringTokenizer st = new StringTokenizer(param, " ");
+
+ if (st.countTokens() < 2)
+ {
+ String sequence = applet.getParameter("PDBSEQ");
+ if (sequence != null)
+ seqs = new SequenceI[]
+ { matcher == null ? (Sequence) newAlignFrame
+ .getAlignViewport().getAlignment()
+ .findName(sequence) : matcher.findIdMatch(sequence) };
+
+ }
+ else
+ {
+ param = st.nextToken();
+ Vector tmp = new Vector();
+ Vector tmp2 = new Vector();
+
+ while (st.hasMoreTokens())
+ {
+ seqstring = st.nextToken();
+ StringTokenizer st2 = new StringTokenizer(seqstring, "=");
+ if (st2.countTokens() > 1)
+ {
+ // This is the chain
+ tmp2.addElement(st2.nextToken());
+ seqstring = st2.nextToken();
+ }
+ tmp.addElement(matcher == null ? (Sequence) newAlignFrame
+ .getAlignViewport().getAlignment()
+ .findName(seqstring) : matcher
+ .findIdMatch(seqstring));
+ }
+
+ seqs = new SequenceI[tmp.size()];
+ tmp.copyInto(seqs);
+ if (tmp2.size() == tmp.size())
+ {
+ chains = new String[tmp2.size()];
+ tmp2.copyInto(chains);
+ }
+ }
+ param = setProtocolState(param);
+
+ if (// !jmolAvailable
+ // &&
+ protocol == AppletFormatAdapter.CLASSLOADER
+ && !useXtrnalSviewer)
+ {
+ // Re: JAL-357 : the bug isn't a problem if we are using an
+ // external viewer!
+ // TODO: verify this Re:
+ // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
+ // This exception preserves the current behaviour where, even if
+ // the local pdb file was identified in the class loader
+ protocol = AppletFormatAdapter.URL; // this is probably NOT
+ // CORRECT!
+ param = addProtocol(param); //
+ }
+
+ pdb.setFile(param);
+
+ if (seqs != null)
+ {
+ for (int i = 0; i < seqs.length; i++)
+ {
+ if (seqs[i] != null)
+ {
+ ((Sequence) seqs[i]).addPDBId(pdb);
+ }
+ else
+ {
+ if (JalviewLite.debug)
+ {
+ // this may not really be a problem but we give a warning
+ // anyway
+ System.err
+ .println("Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "
+ + i + ")");
+ }
+ }
+ }
+
+ if (!alignPdbStructures)
+ {
+ newAlignFrame.newStructureView(applet, pdb, seqs, chains,
+ protocol);
+ }
+ else
+ {
+ pdbs.addElement(new Object[]
+ { pdb, seqs, chains, new String(protocol) });
+ }
+ }
+ }
+
+ pdbFileCount++;
+ } while (param != null || 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 = applet.getParameter("hidefeaturegroups");
+ if (param != null)
+ {
+ applet.setFeatureGroupStateOn(newAlignFrame, param, false);
+ }
+ // show specific groups
+ param = applet.getParameter("showfeaturegroups");
+ if (param != null)
+ {
+ applet.setFeatureGroupStateOn(newAlignFrame, param, true);
+ }
+ }
+ else
+ {
+ fileFound = false;
+ applet.remove(launcher);
+ applet.repaint();
+ }
+ callInitCallback();
+ }
+
+ /**
+ * Discovers whether the given file is in the Applet Archive
+ *
+ * @param file
+ * String
+ * @return boolean
+ */
+ boolean inArchive(String file)
+ {
+ // This might throw a security exception in certain browsers
+ // Netscape Communicator for instance.
+ try
+ {
+ boolean rtn = (getClass().getResourceAsStream("/" + file) != null);
+ if (debug)
+ {
+ System.err.println("Resource '" + file + "' was "
+ + (rtn ? "" : "not") + " located by classloader.");
+ }
+ return rtn;
+ } catch (Exception ex)
+ {
+ System.out.println("Exception checking resources: " + file + " "
+ + ex);
+ return false;
+ }
+ }
+
+ String addProtocol(String file)
+ {
+ if (file.indexOf("://") == -1)
+ {
+ String fl = applet.resolveUrlForLocalOrAbsolute(file,
+ getDocumentBase());
+ try
+ {
+ if (new java.net.URL(fl).openStream() != null)
+ {
+ if (debug)
+ {
+ System.err.println("Prepended document base for resource: '"
+ + file + "'");
+ }
+ return fl;
+ }
+ } catch (Exception x)
+ {
+ }
+ ;
+ fl = applet.resolveUrlForLocalOrAbsolute(file, getCodeBase());
+ try
+ {
+ if (new java.net.URL(fl).openStream() != null)
+ {
+ if (debug)
+ {
+ System.err.println("Prepended codebase for resource: '"
+ + file + "'");
+ }
+ return fl;
+ }
+ } catch (Exception x)
+ {
+ }
+ ;
+
+ }
+
+ return file;
+ }
+ }
+
+ /**
+ * @return the default alignFrame acted on by the public applet methods. May
+ * return null with an error message on System.err indicating the
+ * fact.
+ */
+ public AlignFrame getDefaultTargetFrame()
+ {
+ if (currentAlignFrame != null)
+ {
+ return currentAlignFrame;
+ }
+ if (initialAlignFrame != null)
+ {
+ return initialAlignFrame;
+ }
+ System.err
+ .println("Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");
+ return null;
+ }
+
+ /**
+ * separator used for separatorList
+ */
+ protected String separator = "" + ((char) 0x00AC); // the default used to be
+ // '|' but many sequence
+ // IDS include pipes.
+
+ /**
+ * set to enable the URL based javascript execution mechanism
+ */
+ public boolean jsfallbackEnabled = false;
+
+ /**
+ * parse the string into a list
+ *
+ * @param list
+ * @return elements separated by separator
+ */
+ 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("") || list.equals(separator))
+ return null;
+ java.util.Vector jv = new Vector();
+ int cp = 0, pos;
+ while ((pos = list.indexOf(separator, cp)) > cp)
+ {
+ jv.addElement(list.substring(cp, pos));
+ cp = pos + seplen;
+ }
+ if (cp < list.length())
+ {
+ String c = list.substring(cp);
+ if (!c.equals(separator))
+ {
+ jv.addElement(c);
+ }
+ }
+ if (jv.size() > 0)
+ {
+ String[] v = new String[jv.size()];
+ for (int i = 0; i < v.length; i++)
+ {
+ v[i] = (String) jv.elementAt(i);
+ }
+ jv.removeAllElements();
+ if (debug)
+ {
+ System.err.println("Array from '" + separator
+ + "' separated List:\n" + v.length);
+ for (int i = 0; i < v.length; i++)
+ {
+ System.err.println("item " + i + " '" + v[i] + "'");
+ }
+ }
+ return v;
+ }
+ if (debug)
+ {
+ System.err.println("Empty Array from '" + separator
+ + "' separated List");
+ }
+ return null;
+ }
+
+ /**
+ * concatenate the list with separator
+ *
+ * @param list
+ * @return concatenated string
+ */
+ 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 && list.length > 0)
+ {
+ for (int i = 0, iSize = list.length; i < iSize; i++)
+ {
+ if (list[i] != null)
+ {
+ if (i > 0)
+ {
+ v.append(separator);
+ }
+ v.append(list[i]);
+ }
+ }
+ if (debug)
+ {
+ System.err.println("Returning '" + separator
+ + "' separated List:\n");
+ System.err.println(v);
+ }
+ return v.toString();
+ }
+ if (debug)
+ {
+ System.err.println("Returning empty '" + separator
+ + "' separated List\n");
+ }
+ return "" + separator;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getFeatureGroups()
+ */
+ public String getFeatureGroups()
+ {
+ String lst = arrayToSeparatorList(getDefaultTargetFrame()
+ .getFeatureGroups());
+ return lst;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOn(jalview.appletgui.AlignFrame
+ * )
+ */
+ public String getFeatureGroupsOn(AlignFrame alf)
+ {
+ String lst = arrayToSeparatorList(alf.getFeatureGroups());
+ return lst;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfState(boolean)
+ */
+ public String getFeatureGroupsOfState(boolean visible)
+ {
+ return arrayToSeparatorList(getDefaultTargetFrame()
+ .getFeatureGroupsOfState(visible));
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfStateOn(jalview.appletgui
+ * .AlignFrame, boolean)
+ */
+ public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
+ {
+ return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupStateOn(jalview.appletgui.
+ * AlignFrame, java.lang.String, boolean)
+ */
+ public void setFeatureGroupStateOn(final AlignFrame alf,
+ final String groups, boolean state)
+ {
+ final boolean st = state;// !(state==null || state.equals("") ||
+ // state.toLowerCase().equals("false"));
+ java.awt.EventQueue.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ alf.setFeatureGroupState(separatorListToArray(groups), st);
+ }
+ });
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupState(java.lang.String,
+ * boolean)
+ */
+ public void setFeatureGroupState(String groups, boolean state)
+ {
+ setFeatureGroupStateOn(getDefaultTargetFrame(), groups, state);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getSeparator()
+ */
+ public String getSeparator()
+ {
+ return separator;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#setSeparator(java.lang.String)
+ */
+ 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;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#addPdbFile(jalview.appletgui.AlignFrame,
+ * java.lang.String, java.lang.String, java.lang.String)
+ */
+ 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();
+ }
+
+ private Hashtable jshashes = new Hashtable();
+
+ private Hashtable> jsmessages = new Hashtable>();
+
+ public void setJsMessageSet(String messageclass, String viewId,
+ String[] colcommands)
+ {
+ Hashtable msgset = jsmessages.get(messageclass);
+ if (msgset == null)
+ {
+ msgset = new Hashtable();
+ jsmessages.put(messageclass, msgset);
+ }
+ msgset.put(viewId, colcommands);
+ long[] l = new long[colcommands.length];
+ for (int i = 0; i < colcommands.length; i++)
+ {
+ l[i] = colcommands[i].hashCode();
+ }
+ jshashes.put(messageclass + "|" + viewId, l);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getJsMessage(java.lang.String,
+ * java.lang.String)
+ */
+ public String getJsMessage(String messageclass, String viewId)
+ {
+ Hashtable msgset = jsmessages.get(messageclass);
+ if (msgset != null)
+ {
+ String[] msgs = msgset.get(viewId);
+ if (msgs != null)
+ {
+ for (int i = 0; i < msgs.length; i++)
+ {
+ if (msgs[i] != null)
+ {
+ String m = msgs[i];
+ msgs[i] = null;
+ return m;
+ }
+ }
+ }
+ }
+ return "";
+ }
+
+ public boolean isJsMessageSetChanged(String string, String string2,
+ String[] colcommands)
+ {
+ long[] l = jshashes.get(string + "|" + string2);
+ if (l == null && colcommands != null)
+ {
+ return true;
+ }
+ for (int i = 0; i < colcommands.length; i++)
+ {
+ if (l[i] != colcommands[i].hashCode())
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ private Vector jsExecQueue = new Vector();
+
+ public Vector getJsExecQueue()
+ {
+ return jsExecQueue;
+ }
+
+ public void setExecutor(JSFunctionExec jsFunctionExec2)
+ {
+ jsFunctionExec = jsFunctionExec2;
+ }
+
+ /**
+ * return the given colour value parameter or the given default if parameter
+ * not given
+ *
+ * @param colparam
+ * @param defcolour
+ * @return
+ */
+ public Color getDefaultColourParameter(String colparam, Color defcolour)
+ {
+ String colprop = getParameter(colparam);
+ if (colprop == null || colprop.trim().length() == 0)
+ {
+ return defcolour;
+ }
+ Color col = jalview.schemes.ColourSchemeProperty
+ .getAWTColorFromName(colprop);
+ if (col == null)
+ {
+ try
+ {
+ col = new jalview.schemes.UserColourScheme(colprop).findColour('A');
+ } catch (Exception ex)
+ {
+ System.err.println("Couldn't parse '" + colprop
+ + "' as a colour for " + colparam);
+ col = null;
+ }
+ }
+ return (col == null) ? defcolour : col;
+
+ }
+
+ public void openJalviewHelpUrl()
+ {
+ String helpUrl = getParameter("jalviewhelpurl");
+ if (helpUrl == null || helpUrl.trim().length() < 5)
+ {
+ helpUrl = "http://www.jalview.org/help.html";
+ }
+ showURL(helpUrl, "HELP");
+ }
+
+ /**
+ * form a complete URL given a path to a resource and a reference location on
+ * the same server
+ *
+ * @param url
+ * - an absolute path on the same server as localref or a document
+ * located relative to localref
+ * @param localref
+ * - a URL on the same server as url
+ * @return a complete URL for the resource located by url
+ */
+ private String resolveUrlForLocalOrAbsolute(String url, URL localref)
+ {
+ String codebase = localref.toString();
+ if (url.indexOf("/") == 0)
+ {
+ url = codebase.substring(0, codebase.length()
+ - localref.getFile().length())
+ + url;
+ }
+ else
+ {
+ url = localref + url;
+ }
+ return url;
+ }
+
+ /**
+ * open a URL in the browser - resolving it according to relative refs and
+ * coping with javascript: protocol if necessary.
+ *
+ * @param url
+ * @param target
+ */
+ public void showURL(String url, String target)
+ {
+ try
+ {
+ if (url.indexOf(":") == -1)
+ {
+ // TODO: verify (Bas Vroling bug) prepend codebase or server URL to
+ // form valid URL
+ // Should really use docbase, not codebase.
+ URL prepend;
+ url = resolveUrlForLocalOrAbsolute(
+ url,
+ prepend = getDefaultParameter("resolvetocodebase", false) ? getDocumentBase()
+ : getCodeBase());
+ if (debug)
+ {
+ System.err
+ .println("Show url (prepended "
+ + prepend
+ + " - toggle resolvetocodebase if code/docbase resolution is wrong): "
+ + url);
+ }
+ }
+ else
+ {
+ if (debug)
+ {
+ System.err.println("Show url: " + url);
+ }
+ }
+ if (url.indexOf("javascript:") == 0)
+ {
+ // no target for the javascript context
+ getAppletContext().showDocument(new java.net.URL(url));
+ }
+ else
+ {
+ getAppletContext().showDocument(new java.net.URL(url), target);
+ }
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ /**
+ * 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; }
+ */
+}