/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview - 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 <http://www.gnu.org/licenses/>.
*/
package jalview.bin;
-import java.applet.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.util.*;
-
-import jalview.appletgui.*;
-import jalview.datamodel.*;
-import jalview.io.*;
+import jalview.api.SequenceStructureBinding;
+import jalview.appletgui.AlignFrame;
+import jalview.appletgui.AppletJmol;
+import jalview.appletgui.EmbmenuFrame;
+import jalview.appletgui.FeatureSettings;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+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 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.lang.reflect.Method;
+import java.util.Enumeration;
+import java.util.StringTokenizer;
+import java.util.Vector;
/**
* Jalview Applet. Runs in Java 1.18 runtime
- *
+ *
* @author $author$
* @version $Revision$
*/
-public class JalviewLite
- extends Applet
+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 "¬"
+ * (¬)
+ */
+ public String getSelectedSequences()
+ {
+ return getSelectedSequencesFrom(getDefaultTargetFrame());
+ }
+ /**
+ * @param sep
+ * separator string or null for default
+ * @return String list of selected sequence IDs, each terminated by sep or
+ * ("¬" as default)
+ */
+ public String getSelectedSequences(String sep)
+ {
+ return getSelectedSequencesFrom(getDefaultTargetFrame(), sep);
+ }
- ///////////////////////////////////////////
- //The following public methods maybe called
- //externally, eg via javascript in HTML page
+ /**
+ * @param alf
+ * alignframe containing selection
+ * @return String list of selected sequence IDs, each terminated by "¬"
+ *
+ */
+ public String getSelectedSequencesFrom(AlignFrame alf)
+ {
+ return getSelectedSequencesFrom(alf, "¬");
+ }
- public String getSelectedSequences()
+ /**
+ * get list of selected sequence IDs separated by given separator
+ *
+ * @param alf
+ * window containing selection
+ * @param sep
+ * separator string to use - default is "¬"
+ * @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 (initialAlignFrame.viewport.getSelectionGroup() != null)
+ if (sep == null || sep.length() == 0)
+ {
+ sep = "¬";
+ }
+ if (alf.viewport.getSelectionGroup() != null)
{
- SequenceI[] seqs = initialAlignFrame.viewport.getSelectionGroup().
- getSequencesInOrder(
- initialAlignFrame.viewport.getAlignment());
+ SequenceI[] seqs = alf.viewport.getSelectionGroup()
+ .getSequencesInOrder(alf.viewport.getAlignment());
for (int i = 0; i < seqs.length; i++)
{
- result.append(seqs[i].getName() + "¬");
+ result.append(seqs[i].getName());
+ result.append(sep);
}
}
return result.toString();
}
+ /**
+ * 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(currentAlignFrame, 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 getAlignment(format, "true");
+ 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,
- currentAlignFrame.viewport.getAlignment(), seqlimits);
+ alf.viewport.getAlignment(), seqlimits);
return reply;
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
return "Error retrieving alignment in " + format + " format. ";
public void loadAnnotation(String annotation)
{
- if (new AnnotationFile().readAnnotationFile(
- currentAlignFrame.getAlignViewport().getAlignment(), annotation,
- AppletFormatAdapter.PASTE))
+ loadAnnotationFrom(getDefaultTargetFrame(), annotation);
+ }
+
+ public void loadAnnotationFrom(AlignFrame alf, String annotation)
+ {
+ if (new AnnotationFile().readAnnotationFile(alf.getAlignViewport()
+ .getAlignment(), annotation, AppletFormatAdapter.PASTE))
{
- currentAlignFrame.alignPanel.fontChanged();
- currentAlignFrame.alignPanel.setScrollValues(0, 0);
+ alf.alignPanel.fontChanged();
+ alf.alignPanel.setScrollValues(0, 0);
}
else
{
- currentAlignFrame.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE);
+ alf.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE);
}
}
public String getFeatures(String format)
{
- return currentAlignFrame.outputFeatures(false, format);
+ return getFeaturesFrom(getDefaultTargetFrame(), format);
+ }
+
+ public String getFeaturesFrom(AlignFrame alf, String format)
+ {
+ return alf.outputFeatures(false, format);
}
public String getAnnotation()
{
- return currentAlignFrame.outputAnnotations(false);
+ return getAnnotationFrom(getDefaultTargetFrame());
}
- public void loadAlignment(String text, String title)
+ 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);
+
+ String format = new IdentifyFile().Identify(text,
+ AppletFormatAdapter.PASTE);
try
{
al = new AppletFormatAdapter().readFile(text,
- AppletFormatAdapter.PASTE,
- format);
+ AppletFormatAdapter.PASTE, format);
if (al.getHeight() > 0)
{
- new AlignFrame(al, this, title, false);
+ return new AlignFrame(al, this, title, false);
}
- }
- catch (java.io.IOException ex)
+ } catch (java.io.IOException ex)
{
ex.printStackTrace();
}
+ return null;
}
- ////////////////////////////////////////////////
- ////////////////////////////////////////////////
+ // //////////////////////////////////////////////
+ // //////////////////////////////////////////////
+ public static int lastFrameX = 200;
+ public static int lastFrameY = 200;
- static int lastFrameX = 200;
- 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
- public static AlignFrame currentAlignFrame;
+ /**
+ * 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 static AlignFrame currentAlignFrame = null;
- //This is the first frame to be displayed, and does not change
- AlignFrame initialAlignFrame;
+ /**
+ * 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;
+ }
+
/**
* init method for Jalview Applet
*/
public void init()
{
- try
+
+ /**
+ * turn on extra applet debugging
+ */
+ String dbg = getParameter("debug");
+ if (dbg != null)
{
- if (!System.getProperty("java.version").startsWith("1.1"))
- {
- Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter");
- jmolAvailable = true;
- }
+ debug = dbg.toLowerCase().equals("true");
}
- catch (java.lang.ClassNotFoundException ex)
+ if (debug)
{
- System.out.println("Jmol not available - Using MCview for structures");
- }
+ 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;
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)
+ } catch (Exception ex)
{
r = 255;
g = 255;
if (file == null)
{
- //Maybe the sequences are added as parameters
+ // Maybe the sequences are added as parameters
StringBuffer data = new StringBuffer("PASTE");
int i = 1;
- while ( (file = getParameter("sequence" + i)) != null)
+ while ((file = getParameter("sequence" + i)) != null)
{
data.append(file.toString() + "\n");
i++;
final JalviewLite applet = this;
if (getParameter("embedded") != null
- && getParameter("embedded").equalsIgnoreCase("true"))
+ && getParameter("embedded").equalsIgnoreCase("true"))
{
+ // Launch as embedded applet in page
embedded = true;
LoadingThread loader = new LoadingThread(file, applet);
loader.start();
}
else if (file != null)
{
- add(launcher);
-
- launcher.addActionListener(new java.awt.event.ActionListener()
+ if (getParameter("showbutton") == null
+ || !getParameter("showbutton").equalsIgnoreCase("false"))
{
- public void actionPerformed(ActionEvent e)
+ // Add the JalviewLite 'Button' to the page
+ add(launcher);
+ launcher.addActionListener(new java.awt.event.ActionListener()
{
- LoadingThread loader = new LoadingThread(file,
- applet);
- loader.start();
- }
- });
+ public void actionPerformed(ActionEvent e)
+ {
+ LoadingThread loader = new LoadingThread(file, applet);
+ loader.start();
+ }
+ });
+ }
+ else
+ {
+ // Open jalviewLite immediately.
+ LoadingThread loader = new LoadingThread(file, applet);
+ loader.start();
+ }
}
else
{
+ // jalview initialisation with no alignment. loadAlignment() method can
+ // still be called to open new alignments.
file = "NO FILE";
fileFound = false;
}
}
- public static void main(String[] args)
- {
- if (args.length != 1)
- {
- System.out.println("\nUsage: java -jar jalviewApplet.jar fileName\n");
- System.exit(1);
- }
-
- String format = new jalview.io.IdentifyFile().Identify(args[0],
- AppletFormatAdapter.FILE);
-
- Alignment al = null;
- try
- {
- al = new AppletFormatAdapter().readFile(args[0], AppletFormatAdapter.FILE,
- format);
- }
- catch (java.io.IOException ex)
- {
- ex.printStackTrace();
- }
- if ( (al != null) && (al.getHeight() > 0))
- {
- AlignFrame af = new AlignFrame(al, null, args[0], false);
- af.statusBar.setText("Successfully loaded file " + args[0]);
- }
- }
-
/**
* 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
+ *
+ * @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)
+ int height)
{
frame.setLocation(lastFrameX, lastFrameY);
lastFrameX += 40;
{
if (frame instanceof AlignFrame)
{
- ( (AlignFrame) frame).closeMenuItem_actionPerformed();
+ ((AlignFrame) frame).closeMenuItem_actionPerformed();
}
if (currentAlignFrame == frame)
{
}
lastFrameX -= 40;
lastFrameY -= 40;
+ if (frame instanceof EmbmenuFrame)
+ {
+ ((EmbmenuFrame) frame).destroyMenus();
+ }
frame.setMenuBar(null);
frame.dispose();
}
if (frame instanceof AlignFrame)
{
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"
+ * This paints the background surrounding the "Launch Jalview button" <br>
* <br>
- * <br>If file given in parameter not found, displays error message
- *
- * @param g graphics context
+ * If file given in parameter not found, displays error message
+ *
+ * @param g
+ * graphics context
*/
public void paint(Graphics g)
{
g.drawString("Jalview Applet", 50, this.getSize().height / 2 - 30);
g.drawString("Loading Data...", 50, this.getSize().height / 2);
}
+ }
+
+ 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
+ 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;
- public LoadingThread(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)
{
- file = _file;
if (file.startsWith("PASTE"))
{
file = file.substring(5);
file = addProtocol(file);
protocol = AppletFormatAdapter.URL;
}
- format = new jalview.io.IdentifyFile().Identify(file, protocol);
+ 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();
+ }
+
+ 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)
+ 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))
+ if ((al != null) && (al.getHeight() > 0))
{
- currentAlignFrame = new AlignFrame(al,
- applet,
- file,
- embedded);
+ 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)
{
- currentAlignFrame.setTitle("Sequences from " + getDocumentBase());
+ newAlignFrame.setTitle("Sequences from " + getDocumentBase());
}
- initialAlignFrame = currentAlignFrame;
-
- currentAlignFrame.statusBar.setText("Successfully loaded file " + file);
+ newAlignFrame.statusBar.setText("Successfully loaded file " + file);
String treeFile = applet.getParameter("tree");
if (treeFile == null)
{
try
{
- if (inArchive(treeFile))
- {
- protocol = AppletFormatAdapter.CLASSLOADER;
- }
- else
- {
- protocol = AppletFormatAdapter.URL;
- treeFile = addProtocol(treeFile);
- }
-
+ 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);
+ protocol);
fin.parse();
if (fin.getTree() != null)
{
- currentAlignFrame.loadTree(fin, treeFile);
+ newAlignFrame.loadTree(fin, treeFile);
+ dbgMsg("Successfuly imported tree.");
}
- }
- catch (Exception ex)
+ else
+ {
+ dbgMsg("Tree parameter did not resolve to a valid tree.");
+ }
+ } catch (Exception ex)
{
ex.printStackTrace();
}
String param = getParameter("features");
if (param != null)
{
- if (!inArchive(param))
- {
- param = addProtocol(param);
- }
+ param = setProtocolState(param);
- currentAlignFrame.parseFeaturesFile(param, protocol);
+ newAlignFrame.parseFeaturesFile(param, protocol);
}
param = getParameter("showFeatureSettings");
if (param != null && param.equalsIgnoreCase("true"))
{
- currentAlignFrame.viewport.showSequenceFeatures(true);
- new FeatureSettings(currentAlignFrame.alignPanel);
+ newAlignFrame.viewport.showSequenceFeatures(true);
+ new FeatureSettings(newAlignFrame.alignPanel);
}
param = getParameter("annotations");
if (param != null)
{
- if (!inArchive(param))
+ param = setProtocolState(param);
+
+ if (new AnnotationFile().readAnnotationFile(
+ newAlignFrame.viewport.getAlignment(), param, protocol))
{
- param = addProtocol(param);
+ newAlignFrame.alignPanel.fontChanged();
+ newAlignFrame.alignPanel.setScrollValues(0, 0);
+ }
+ else
+ {
+ System.err
+ .println("Annotations were not added from annotation file '"
+ + param + "'");
}
-
- new AnnotationFile().readAnnotationFile(
- currentAlignFrame.viewport.getAlignment(),
- param,
- protocol);
-
- currentAlignFrame.alignPanel.fontChanged();
- currentAlignFrame.alignPanel.setScrollValues(0, 0);
}
{
try
{
- if (inArchive(param))
- {
- protocol = AppletFormatAdapter.CLASSLOADER;
- }
- else
- {
- protocol = AppletFormatAdapter.URL;
- param = addProtocol(param);
- }
-
+ param = setProtocolState(param);
jalview.io.JPredFile predictions = new jalview.io.JPredFile(
- param, protocol);
- new JnetAnnotationMaker().add_annotation(predictions,
- currentAlignFrame.viewport.getAlignment(),
- 0, false); // do not add sequence profile from concise output
- currentAlignFrame.alignPanel.fontChanged();
- currentAlignFrame.alignPanel.setScrollValues(0, 0);
- }
- catch (Exception ex)
+ 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();
}
}
+ /*
+ * <param name="alignpdbfiles" value="false/true"/>
+ * Undocumented for 2.6 - related to JAL-434
+ */
+ applet.setAlignPdbStructures(getDefaultParameter("alignpdbfiles",false));
+ /*
+ * <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B
+ * PDB|1GAQ|1GAQ|C">
+ *
+ * <param name="PDBfile2" value="1gaq.txt A=SEQA B=SEQB C=SEQB">
+ *
+ * <param name="PDBfile3" value="1q0o Q45135_9MICO">
+ */
+
+ int pdbFileCount = 0;
+ // Accumulate pdbs here if they are heading for the same view (if alignPdbStructures is true)
+ Vector pdbs=new Vector();
+ do
+ {
+ if (pdbFileCount > 0)
+ param = getParameter("PDBFILE" + pdbFileCount);
+ else
+ param = getParameter("PDBFILE");
+ if (param != null)
+ {
+ PDBEntry pdb = new PDBEntry();
- param = getParameter("PDBFILE");
- if (param != null)
- {
+ String seqstring;
+ SequenceI[] seqs = null;
+ String[] chains = null;
- PDBEntry pdb = new PDBEntry();
+ StringTokenizer st = new StringTokenizer(param, " ");
- String seqstring;
- SequenceI [] seqs = null;
+ if (st.countTokens() < 2)
+ {
+ String sequence = applet.getParameter("PDBSEQ");
+ if (sequence != null)
+ seqs = new SequenceI[]
+ { (Sequence) newAlignFrame.getAlignViewport()
+ .getAlignment().findName(sequence) };
- if(param.indexOf(" ")>-1)
- {
- seqstring = param.substring(param.indexOf(" ")+1);
- param = param.substring(0, param.indexOf(" "));
- StringTokenizer st = new StringTokenizer(seqstring);
- Vector tmp = new Vector();
- while(st.hasMoreTokens())
+ }
+ else
{
- tmp.addElement((Sequence) currentAlignFrame.
- getAlignViewport().getAlignment().
- findName(st.nextToken()));
+ 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);
- seqs = new SequenceI[tmp.size()];
- tmp.copyInto(seqs);
- }
- else
- {
- String sequence = applet.getParameter("PDBSEQ");
- if (sequence != null)
- seqs = new SequenceI[]
- {
- (Sequence) currentAlignFrame.
- getAlignViewport().getAlignment().
- findName(sequence)};
- }
+ 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); //
+ }
- if (!inArchive(param) || jmolAvailable)
- {
- param = addProtocol(param);
- }
+ pdb.setFile(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)});
+ }
+ }
+ }
- for(int i=0; i<seqs.length; i++)
+ 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++)
{
- ((Sequence)seqs[i]).addPDBId(pdb);
+ 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];
}
-
- if (jmolAvailable)
- new jalview.appletgui.AppletJmol(pdb,
- seqs,
- currentAlignFrame.alignPanel,
- protocol);
- else
-
- new MCview.AppletPDBViewer(pdb,
- seqs,
- currentAlignFrame.alignPanel,
- protocol);
+ newAlignFrame.alignedStructureView(applet, pdb, seqs, chains, protocols);
+
+ }
+ // ///////////////////////////
+ // modify display of features
+ //
+ // hide specific groups
+ param = getParameter("hidefeaturegroups");
+ if (param != null)
+ {
+ applet.setFeatureGroupStateOn(newAlignFrame, param, false);
+ }
+ // show specific groups
+ param = getParameter("showfeaturegroups");
+ if (param != null)
+ {
+ applet.setFeatureGroupStateOn(newAlignFrame, param, true);
}
}
else
/**
* Discovers whether the given file is in the Applet Archive
- * @param file String
+ *
+ * @param file
+ * String
* @return boolean
*/
boolean inArchive(String file)
{
- //This might throw a security exception in certain browsers
- //Netscape Communicator for instance.
+ // This might throw a security exception in certain browsers
+ // Netscape Communicator for instance.
try
{
- return (getClass().getResourceAsStream("/" + file) != null);
- }
- catch (Exception ex)
+ 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);
+ System.out.println("Exception checking resources: " + file + " "
+ + ex);
return false;
}
}
if (file.indexOf("://") == -1)
{
file = 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.
+ */
+ protected 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 = "|"; // this is a safe(ish) separator - tabs
+
+ // don't work for firefox
+
+ /**
+ * parse the string into a list
+ *
+ * @param list
+ * @return elements separated by separator
+ */
+ public String[] separatorListToArray(String list)
+ {
+ int seplen = separator.length();
+ if (list == null || list.equals(""))
+ 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())
+ {
+ jv.addElement(list.substring(cp));
+ }
+ 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)
+ {
+ StringBuffer v = new StringBuffer();
+ if (list != null && list.length>0)
+ {
+ for (int i = 0, iSize = list.length - 1; i < iSize; i++)
+ {
+ if (list[i] != null)
+ {
+ v.append(list[i]);
+ }
+ v.append(separator);
+ }
+ if (list[list.length - 1] != null)
+ {
+ v.append(list[list.length - 1]);
+ }
+ if (debug)
+ {
+ System.err.println("Returning '" + separator
+ + "' separated List:\n");
+ System.err.println(v);
+ }
+ return v.toString();
+ }
+ if (debug)
+ {
+ System.err.println("Returning empty '" + separator
+ + "' separated List\n");
+ }
+ return "";
+ }
+
+ /**
+ * @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
+ */
+ public void setSeparator(String separator)
+ {
+ this.separator = 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;
+ }
+
+ /**
+ * get all components associated with the applet of the given type
+ * @param class1
+ * @return
+ */
+ public Vector getAppletWindow(Class class1)
+ {
+ Vector wnds = new Vector();
+ Component[] cmp = getComponents();
+ if (cmp!=null)
+ {
+ for (int i=0;i<cmp.length;i++)
+ {
+ if (class1.isAssignableFrom(cmp[i].getClass()))
+ {
+ wnds.addElement(cmp);
+ }
+ }}
+ return wnds;
+ }
+
+
+ /**
+ * bind structures in a viewer to any matching sequences in an alignFrame (use
+ * sequenceIds to limit scope of search to specific sequences)
+ *
+ * @param alFrame
+ * @param viewer
+ * @param sequenceIds
+ * @return TODO: consider making an exception structure for indicating when
+ * binding fails
+ public SequenceStructureBinding addStructureViewInstance(
+ AlignFrame alFrame, Object viewer, String sequenceIds)
+ {
+
+ if (sequenceIds != null && sequenceIds.length() > 0)
+ {
+ return alFrame.addStructureViewInstance(viewer,
+ separatorListToArray(sequenceIds));
+ }
+ else
+ {
+ return alFrame.addStructureViewInstance(viewer, null);
+ }
+ // return null;
+ }
+ */
}
git://source.jalview.org / jalview.git / blobdiff