/*
- * 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 2.5)
+ * 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.awt.*;
import java.awt.event.*;
+import java.io.BufferedReader;
+import java.io.InputStreamReader;
import java.util.*;
+import jalview.api.SequenceStructureBinding;
import jalview.appletgui.*;
import jalview.datamodel.*;
import jalview.io.*;
/**
* @param sep
- * separator string or null for default
+ * separator string or null for default
* @return String list of selected sequence IDs, each terminated by sep or
* ("¬" as default)
*/
/**
* @param alf
- * alignframe containing selection
+ * alignframe containing selection
* @return String list of selected sequence IDs, each terminated by "¬"
*
*/
* get list of selected sequence IDs separated by given separator
*
* @param alf
- * window containing selection
+ * window containing selection
* @param sep
- * separator string to use - default is "¬"
+ * separator string to use - default is "¬"
* @return String list of selected sequence IDs, each terminated by the given
* separator
*/
* get sequences selected in current alignFrame and return their alignment in
* format 'format' either with or without suffix
*
- * @param alf -
- * where selection is
- * @param format -
- * format of alignment file
- * @param suffix -
- * "true" to append /start-end string to each sequence ID
+ * @param alf
+ * - where selection is
+ * @param format
+ * - format of alignment file
+ * @param suffix
+ * - "true" to append /start-end string to each sequence ID
* @return selected sequences as flat file or empty string if there was no
* current selection
*/
* get sequences selected in alf and return their alignment in format 'format'
* either with or without suffix
*
- * @param alf -
- * where selection is
- * @param format -
- * format of alignment file
- * @param suffix -
- * "true" to append /start-end string to each sequence ID
+ * @param alf
+ * - where selection is
+ * @param format
+ * - format of alignment file
+ * @param suffix
+ * - "true" to append /start-end string to each sequence ID
* @return selected sequences as flat file or empty string if there was no
* current selection
*/
/**
*
* @param text
- * alignment file as a string
+ * alignment file as a string
* @param title
- * window title
+ * window title
* @return null or new alignment frame
*/
public AlignFrame loadAlignment(String text, String title)
{
Alignment al = null;
+
String format = new IdentifyFile().Identify(text,
AppletFormatAdapter.PASTE);
try
* AlignFrame if the applet is started as embedded on the page and then
* afterwards a new view is created.
*/
- public static AlignFrame currentAlignFrame;
+ public static 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;
+ 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;
- public static boolean debug;
+ 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()
{
+
/**
* turn on extra applet debugging
*/
{
debug = dbg.toLowerCase().equals("true");
}
+ if (debug)
+ {
+
+ System.err.println("JalviewLite Version " + getVersion());
+ System.err.println("Build Date : " + getBuildDate());
+
+ }
/**
* if true disable the check for jmol
*/
String chkforJmol = getParameter("nojmol");
- if (chkforJmol!=null)
+ if (chkforJmol != null)
{
checkForJmol = !chkforJmol.equals("true");
}
}
}
- LoadJmolThread jmolAvailable = new LoadJmolThread();
- jmolAvailable.start();
-
final JalviewLite applet = this;
if (getParameter("embedded") != null
&& getParameter("embedded").equalsIgnoreCase("true"))
* Initialises and displays a new java.awt.Frame
*
* @param frame
- * java.awt.Frame to be displayed
+ * java.awt.Frame to be displayed
* @param title
- * title of new frame
+ * title of new frame
* @param width
- * width if new frame
+ * width if new frame
* @param height
- * height of new frame
+ * height of new frame
*/
public static void addFrame(final Frame frame, String title, int width,
int height)
/*
* Probably not necessary to do this - see TODO above. (non-Javadoc)
*
- * @see java.awt.event.WindowAdapter#windowDeactivated(java.awt.event.WindowEvent)
+ * @see
+ * java.awt.event.WindowAdapter#windowDeactivated(java.awt.event.WindowEvent
+ * )
*
* public void windowDeactivated(WindowEvent e) { if (currentAlignFrame ==
* frame) { currentAlignFrame = null; if (debug) {
* If file given in parameter not found, displays error message
*
* @param g
- * graphics context
+ * graphics context
*/
public void paint(Graphics g)
{
class LoadJmolThread extends Thread
{
+ private boolean running = false;
+
public void run()
{
+ if (running || checkedForJmol)
+ {
+ return;
+ }
+ running = true;
if (checkForJmol)
{
try
} catch (java.lang.ClassNotFoundException ex)
{
}
- } else {
- jmolAvailable=false;
+ }
+ else
+ {
+ jmolAvailable = false;
if (debug)
{
- System.err.println("Skipping Jmol check. Will use MCView (probably)");
+ System.err
+ .println("Skipping Jmol check. Will use MCView (probably)");
}
}
+ checkedForJmol = true;
+ running = false;
+ }
+
+ public boolean notFinished()
+ {
+ return running || !checkedForJmol;
}
}
*/
String format;
+ String _file;
+
JalviewLite applet;
private void dbgMsg(String msg)
public LoadingThread(String _file, JalviewLite _applet)
{
- 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 + "'");
+ 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
{
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.");
- initialAlignFrame = new AlignFrame(al, applet, file, embedded);
+ newAlignFrame = new AlignFrame(al, applet, file, embedded);
+ if (initialAlignFrame == null)
+ {
+ initialAlignFrame = newAlignFrame;
+ }
// update the focus.
- currentAlignFrame = initialAlignFrame;
+ currentAlignFrame = newAlignFrame;
if (protocol == jalview.io.AppletFormatAdapter.PASTE)
{
- currentAlignFrame.setTitle("Sequences from " + getDocumentBase());
+ newAlignFrame.setTitle("Sequences from " + getDocumentBase());
}
- currentAlignFrame.statusBar.setText("Successfully loaded file "
- + file);
+ newAlignFrame.statusBar.setText("Successfully loaded file " + file);
String treeFile = applet.getParameter("tree");
if (treeFile == null)
if (fin.getTree() != null)
{
- currentAlignFrame.loadTree(fin, treeFile);
+ newAlignFrame.loadTree(fin, treeFile);
dbgMsg("Successfuly imported tree.");
}
else
{
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");
param = setProtocolState(param);
if (new AnnotationFile().readAnnotationFile(
- currentAlignFrame.viewport.getAlignment(), param,
- protocol))
+ newAlignFrame.viewport.getAlignment(), param, protocol))
{
- currentAlignFrame.alignPanel.fontChanged();
- currentAlignFrame.alignPanel.setScrollValues(0, 0);
+ newAlignFrame.alignPanel.fontChanged();
+ newAlignFrame.alignPanel.setScrollValues(0, 0);
}
else
{
jalview.io.JPredFile predictions = new jalview.io.JPredFile(
param, protocol);
JnetAnnotationMaker.add_annotation(predictions,
- currentAlignFrame.viewport.getAlignment(), 0, false); // false==do
- // not
- // add
- // sequence
- // profile
- // from
- // concise
- // output
- currentAlignFrame.alignPanel.fontChanged();
- currentAlignFrame.alignPanel.setScrollValues(0, 0);
+ 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();
String sequence = applet.getParameter("PDBSEQ");
if (sequence != null)
seqs = new SequenceI[]
- { (Sequence) currentAlignFrame.getAlignViewport()
+ { (Sequence) newAlignFrame.getAlignViewport()
.getAlignment().findName(sequence) };
}
tmp2.addElement(st2.nextToken());
seqstring = st2.nextToken();
}
- tmp.addElement((Sequence) currentAlignFrame
- .getAlignViewport().getAlignment().findName(
- seqstring));
+ tmp.addElement((Sequence) newAlignFrame.getAlignViewport()
+ .getAlignment().findName(seqstring));
}
seqs = new SequenceI[tmp.size()];
}
param = setProtocolState(param);
- if (!jmolAvailable
- && protocol == AppletFormatAdapter.CLASSLOADER)
+ if (// !jmolAvailable
+ // &&
+ protocol == AppletFormatAdapter.CLASSLOADER)
{
- // TODO: pass PDB file in classloader on to Jmol
+ // 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!
+ // CORRECT!
param = addProtocol(param); //
}
if (jmolAvailable)
{
new jalview.appletgui.AppletJmol(pdb, seqs, chains,
- currentAlignFrame.alignPanel, protocol);
+ newAlignFrame.alignPanel, protocol);
lastFrameX += 40;
lastFrameY += 40;
}
else
new MCview.AppletPDBViewer(pdb, seqs, chains,
- currentAlignFrame.alignPanel, protocol);
+ newAlignFrame.alignPanel, protocol);
}
}
param = getParameter("hidefeaturegroups");
if (param != null)
{
- applet.setFeatureGroupState(param, false);
+ applet.setFeatureGroupStateOn(newAlignFrame, param, false);
}
// show specific groups
param = getParameter("showfeaturegroups");
if (param != null)
{
- applet.setFeatureGroupState(param, true);
+ applet.setFeatureGroupStateOn(newAlignFrame, param, true);
}
}
else
* Discovers whether the given file is in the Applet Archive
*
* @param file
- * String
+ * String
* @return boolean
*/
boolean inArchive(String file)
* separator used for separatorList
*/
protected String separator = "|"; // this is a safe(ish) separator - tabs
- // don't work for firefox
+
+ // don't work for firefox
/**
* parse the string into a list
/**
* @param alf
- * alignframe to get feature groups on
+ * alignframe to get feature groups on
* @return
* @see jalview.appletgui.AlignFrame#getFeatureGroups()
*/
/**
* @param alf
- * align frame to get groups of state visible
+ * align frame to get groups of state visible
* @param visible
* @return
* @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)
/**
* @param groups
- * tab separated list of group names
+ * tab separated list of group names
* @param state
- * true or false
+ * true or false
* @see jalview.appletgui.AlignFrame#setFeatureGroupState(java.lang.String[],
* boolean)
*/
boolean state)
{
boolean st = state;// !(state==null || state.equals("") ||
- // state.toLowerCase().equals("false"));
+ // state.toLowerCase().equals("false"));
alf.setFeatureGroupState(separatorListToArray(groups), st);
}
* List separator string
*
* @param separator
- * the separator to set
+ * 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)
+ {
+ System.err.println("addPdbFile not yet implemented.");
+ return true;
+ }
+ /**
+ * bind the viewer instance to the pdbFile associated with sequences in the given alFrame.
+ * @param alFrame
+ * @param pdbFile - pdbFile URI as given via applet's parameters or by addPdb
+ * @param viewer
+ * @return binding for viewer
+ * TODO: consider making an exception structure for indicating when binding fails
+ */
+ public SequenceStructureBinding addJmolInstance(AlignFrame alFrame, String pdbFile, org.jmol.api.JmolViewer viewer)
+ {
+ System.err.println("addJmolInstance not yet implemented.");
+ /**
+ */
+ return null;
+ }
+ /**
+ * bind structures in a viewer to any matching sequences in an alignFrame (use seuqenceIds to limit scope of search to specific sequences)
+ * @param alFrame
+ * @param viewer
+ * @param sequenceIds
+ * @return
+ */
+ public SequenceStructureBinding addJmolInstance(AlignFrame alFrame, org.jmol.api.JmolViewer viewer, String sequenceIds)
+ {
+ if (viewer!=null)
+ {
+ if (sequenceIds!=null && sequenceIds.length()>0)
+ {
+ return alFrame.addJmolInstance(viewer, separatorListToArray(sequenceIds));
+ } else {
+ return alFrame.addJmolInstance(viewer, null);
+ }
+ }
+ return null;
+ }
}
git://source.jalview.org / jalview.git / blobdiff