/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 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.ws;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
import java.util.*;
import javax.swing.*;
import jalview.analysis.*;
import jalview.bin.*;
import jalview.datamodel.*;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentView;
import jalview.gui.*;
-import jalview.io.*;
-import jalview.util.*;
-import jalview.ws.WSThread.*;
-import vamsas.objects.simple.*;
-public class JPredClient
- extends WSClient
+public class JPredClient extends WS1Client
{
- /**
- * crate a new GUI JPred Job
- * @param sh ServiceHandle
- * @param title String
- * @param msa boolean - true - submit alignment as a sequence profile
- * @param alview AlignmentView
- * @param viewonly TODO
- */
- public JPredClient(ext.vamsas.ServiceHandle sh, String title, boolean msa, AlignmentView alview, AlignFrame parentFrame, boolean viewonly) {
+ /**
+ * crate a new GUI JPred Job
+ *
+ * @param sh
+ * ServiceHandle
+ * @param title
+ * String
+ * @param msa
+ * boolean - true - submit alignment as a sequence profile
+ * @param alview
+ * AlignmentView
+ * @param viewonly
+ * TODO
+ */
+ public JPredClient(ext.vamsas.ServiceHandle sh, String title,
+ boolean msa, AlignmentView alview, AlignFrame parentFrame,
+ boolean viewonly)
+ {
super();
- wsInfo=setWebService(sh);
+ wsInfo = setWebService(sh);
startJPredClient(title, msa, alview, parentFrame, viewonly);
}
+
/**
- * startJPredClient
- * TODO: refine submission to cope with local prediction of visible regions or multiple single sequence jobs
- * TODO: sequence representative support - could submit alignment of representatives as msa.
- * TODO: msa hidden region prediction - submit each chunk for prediction. concatenate results of each.
- * TODO: single seq prediction - submit each contig of each sequence for prediction (but must cope with flanking regions and short seqs)
- * @param title String
- * @param msa boolean
- * @param alview AlignmentView
- * @param viewonly if true then the prediction will be made just on the concatenated visible regions
+ * startJPredClient TODO: refine submission to cope with local prediction of
+ * visible regions or multiple single sequence jobs TODO: sequence
+ * representative support - could submit alignment of representatives as msa.
+ * TODO: msa hidden region prediction - submit each chunk for prediction.
+ * concatenate results of each. TODO: single seq prediction - submit each
+ * contig of each sequence for prediction (but must cope with flanking regions
+ * and short seqs)
+ *
+ * @param title
+ * String
+ * @param msa
+ * boolean
+ * @param alview
+ * AlignmentView
+ * @param viewonly
+ * if true then the prediction will be made just on the concatenated
+ * visible regions
*/
private void startJPredClient(String title, boolean msa,
- jalview.datamodel.AlignmentView alview, AlignFrame parentFrame, boolean viewonly)
+ jalview.datamodel.AlignmentView alview, AlignFrame parentFrame,
+ boolean viewonly)
{
AlignmentView input = alview;
if (wsInfo == null)
Cache.log.warn("Couldn't find a Jpred webservice to invoke!");
return;
}
- SeqCigar[] msf=null;
- SequenceI seq=null;
- int[] delMap=null;
+ SeqCigar[] msf = null;
+ SequenceI seq = null;
+ int[] delMap = null;
// original JNetClient behaviour - submit full length of sequence or profile
// and mask result.
msf = input.getSequences();
seq = msf[0].getSeq('-');
- if (viewonly) {
+ if (viewonly)
+ {
int[] viscontigs = alview.getVisibleContigs();
- int spos=0;
- int i=0;
- if (viscontigs!=null) {
- // Construct the delMap - mapping from the positions within the input to Jnet to the contigs in the original sequence
-
- delMap = new int[seq.getEnd()-seq.getStart()+1];
+ int spos = 0;
+ int i = 0;
+ if (viscontigs != null)
+ {
+ // Construct the delMap - mapping from the positions within the input to
+ // Jnet to the contigs in the original sequence
+
+ delMap = new int[seq.getEnd() - seq.getStart() + 1];
int gapMap[] = seq.gapMap();
- for (int contig = 0; contig<viscontigs.length; contig += 2)
+ for (int contig = 0; contig < viscontigs.length; contig += 2)
{
-
- while (spos<gapMap.length && gapMap[spos]<viscontigs[contig]) {
+
+ while (spos < gapMap.length && gapMap[spos] < viscontigs[contig])
+ {
spos++;
}
- while (spos<gapMap.length && gapMap[spos]<=viscontigs[contig+1]) {
+ while (spos < gapMap.length
+ && gapMap[spos] <= viscontigs[contig + 1])
+ {
delMap[i++] = spos++;
}
}
int tmap[] = new int[i];
System.arraycopy(delMap, 0, tmap, 0, i);
- delMap=tmap;
- }
+ delMap = tmap;
+ }
}
if (msa && msf.length > 1)
{
-
- String altitle = "JNet prediction on "+(viewonly?"visible ":"") + seq.getName() +
- " using alignment from " + title;
+
+ String altitle = getPredictionName(WebServiceName) + " on "
+ + (viewonly ? "visible " : "") + seq.getName()
+ + " using alignment from " + title;
SequenceI aln[] = new SequenceI[msf.length];
for (int i = 0, j = msf.length; i < j; i++)
{
aln[i] = msf[i].getSeq('-');
}
-
-
- Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, true);
- if (viewonly) {
+
+ Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln,
+ true);
+ if (viewonly)
+ {
// Remove hidden regions from sequence objects.
String seqs[] = alview.getSequenceStrings('-');
for (int i = 0, j = msf.length; i < j; i++)
- {
+ {
aln[i].setSequence(seqs[i]);
- }
+ }
seq.setSequence(seqs[0]);
- }
- wsInfo.setProgressText("Job details for "+(viewonly?"visible ":"")+"MSA based prediction (" +
- title + ") on sequence :\n>" + seq.getName() +
- "\n" +
- AlignSeq.extractGaps("-. ", seq.getSequence()) +
- "\n");
+ }
+ wsInfo.setProgressText("Job details for "
+ + (viewonly ? "visible " : "") + "MSA based prediction ("
+ + title + ") on sequence :\n>" + seq.getName() + "\n"
+ + AlignSeq.extractGaps("-. ", seq.getSequenceAsString())
+ + "\n");
JPredThread jthread = new JPredThread(wsInfo, altitle, server,
- SequenceInfo, aln, delMap, alview, parentFrame, WsURL);
+ SequenceInfo, aln, delMap, alview, parentFrame, WsURL);
wsInfo.setthisService(jthread);
jthread.start();
}
else
{
- if (!msa && msf.length>1)
- throw new Error("Implementation Error! Multiple single sequence prediction jobs are not yet supported.");
- String altitle = "JNet prediction for "+(viewonly?"visible ":"")+"sequence " + seq.getName() +
- " from " +
- title;
+ if (!msa && msf.length > 1)
+ {
+ throw new Error(
+ "Implementation Error! Multiple single sequence prediction jobs are not yet supported.");
+ }
+
+ String altitle = getPredictionName(WebServiceName) + " for "
+ + (viewonly ? "visible " : "") + "sequence " + seq.getName()
+ + " from " + title;
String seqname = seq.getName();
- Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(
- seq);
- if (viewonly) {
+ Hashtable SequenceInfo = jalview.analysis.SeqsetUtils
+ .SeqCharacterHash(seq);
+ if (viewonly)
+ {
// Remove hidden regions from input sequence
String seqs[] = alview.getSequenceStrings('-');
seq.setSequence(seqs[0]);
- }
- wsInfo.setProgressText("Job details for prediction on "+(viewonly?"visible ":"")+"sequence :\n>" +
- seqname + "\n" +
- AlignSeq.extractGaps("-. ", seq.getSequence()) +
- "\n");
+ }
+ wsInfo.setProgressText("Job details for prediction on "
+ + (viewonly ? "visible " : "") + "sequence :\n>" + seqname
+ + "\n"
+ + AlignSeq.extractGaps("-. ", seq.getSequenceAsString())
+ + "\n");
JPredThread jthread = new JPredThread(wsInfo, altitle, server, WsURL,
- SequenceInfo, seq, delMap, alview, parentFrame);
+ SequenceInfo, seq, delMap, alview, parentFrame);
wsInfo.setthisService(jthread);
jthread.start();
}
}
- public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI seq, AlignFrame parentFrame)
+
+ private String getPredictionName(String webServiceName)
+ {
+ if (webServiceName.toLowerCase().indexOf(
+ "secondary structure prediction") > -1)
+ {
+ return webServiceName;
+ }
+ else
+ {
+ return webServiceName + "secondary structure prediction";
+ }
+ }
+
+ public JPredClient(ext.vamsas.ServiceHandle sh, String title,
+ SequenceI seq, AlignFrame parentFrame)
{
super();
wsInfo = setWebService(sh);
startJPredClient(title, seq, parentFrame);
}
- public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI[] msa, AlignFrame parentFrame)
+ public JPredClient(ext.vamsas.ServiceHandle sh, String title,
+ SequenceI[] msa, AlignFrame parentFrame)
{
wsInfo = setWebService(sh);
startJPredClient(title, msa, parentFrame);
startJPredClient(title, seq, null);
}
- private void startJPredClient(String title, SequenceI[] msf, AlignFrame parentFrame)
+ public JPredClient()
+ {
+
+ super();
+ // add a class reference to the list
+ }
+
+ private void startJPredClient(String title, SequenceI[] msf,
+ AlignFrame parentFrame)
{
if (wsInfo == null)
{
SequenceI seq = msf[0];
- String altitle = "JNet prediction on " + seq.getName() +
- " using alignment from " + title;
+ String altitle = "JNet prediction on " + seq.getName()
+ + " using alignment from " + title;
- wsInfo.setProgressText("Job details for MSA based prediction (" +
- title + ") on sequence :\n>" + seq.getName() + "\n" +
- AlignSeq.extractGaps("-. ", seq.getSequence()) +
- "\n");
+ wsInfo
+ .setProgressText("Job details for MSA based prediction ("
+ + title
+ + ") on sequence :\n>"
+ + seq.getName()
+ + "\n"
+ + AlignSeq
+ .extractGaps("-. ", seq.getSequenceAsString())
+ + "\n");
SequenceI aln[] = new SequenceI[msf.length];
for (int i = 0, j = msf.length; i < j; i++)
{
aln[i] = new jalview.datamodel.Sequence(msf[i]);
}
- Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, true);
+ Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln,
+ true);
Jpred server = locateWebService();
- if (server==null)
+ if (server == null)
{
return;
}
- JPredThread jthread = new JPredThread(wsInfo, altitle, server, SequenceInfo, aln,null, null, parentFrame, WsURL);
+ JPredThread jthread = new JPredThread(wsInfo, altitle, server,
+ SequenceInfo, aln, null, null, parentFrame, WsURL);
wsInfo.setthisService(jthread);
jthread.start();
}
- public void startJPredClient(String title, SequenceI seq, AlignFrame parentFrame)
+ public void startJPredClient(String title, SequenceI seq,
+ AlignFrame parentFrame)
{
if (wsInfo == null)
{
wsInfo = setWebService();
}
- wsInfo.setProgressText("Job details for prediction on sequence :\n>" +
- seq.getName() + "\n" +
- AlignSeq.extractGaps("-. ", seq.getSequence()) +
- "\n");
- String altitle = "JNet prediction for sequence " + seq.getName() + " from " +
- title;
+ wsInfo
+ .setProgressText("Job details for prediction on sequence :\n>"
+ + seq.getName()
+ + "\n"
+ + AlignSeq
+ .extractGaps("-. ", seq.getSequenceAsString())
+ + "\n");
+ String altitle = "JNet prediction for sequence " + seq.getName()
+ + " from " + title;
- Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);
+ Hashtable SequenceInfo = jalview.analysis.SeqsetUtils
+ .SeqCharacterHash(seq);
Jpred server = locateWebService();
- if (server==null)
+ if (server == null)
{
return;
}
- JPredThread jthread = new JPredThread(wsInfo, altitle, server, WsURL, SequenceInfo, seq,null, null, parentFrame);
+ JPredThread jthread = new JPredThread(wsInfo, altitle, server, WsURL,
+ SequenceInfo, seq, null, null, parentFrame);
wsInfo.setthisService(jthread);
jthread.start();
}
{
WebServiceName = "JNetWS";
WebServiceJobTitle = "JNet secondary structure prediction";
- WebServiceReference =
- "\"Cuff J. A and Barton G.J (2000) Application of " +
- "multiple sequence alignment profiles to improve protein secondary structure prediction, " +
- "Proteins 40:502-511\".";
+ WebServiceReference = "\"Cuff J. A and Barton G.J (2000) Application of "
+ + "multiple sequence alignment profiles to improve protein secondary structure prediction, "
+ + "Proteins 40:502-511\".";
WsURL = "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred";
WebserviceInfo wsInfo = new WebserviceInfo(WebServiceJobTitle,
- WebServiceReference);
+ WebServiceReference);
return wsInfo;
}
private ext.vamsas.Jpred locateWebService()
{
ext.vamsas.JpredServiceLocator loc = new JpredServiceLocator(); // Default
- ext.vamsas.Jpred server=null;
+ ext.vamsas.Jpred server = null;
try
{
- server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set from properties
- ( (JpredSoapBindingStub)server).setTimeout(60000); // one minute stub
- //((JpredSoapBindingStub)this.server)._setProperty(org.apache.axis.encoding.C, Boolean.TRUE);
+ server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set
+ // from properties
+ ((JpredSoapBindingStub) server).setTimeout(60000); // one minute stub
+ // ((JpredSoapBindingStub)this.server)._setProperty(org.apache.axis.encoding.C,
+ // Boolean.TRUE);
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
JOptionPane.showMessageDialog(Desktop.desktop,
- "The Secondary Structure Prediction Service named " +
- WebServiceName + " at " + WsURL +
- " couldn't be located.",
- "Internal Jalview Error",
- JOptionPane.WARNING_MESSAGE);
- wsInfo.setProgressText("Serious! " + WebServiceName +
- " Service location failed\nfor URL :" + WsURL +
- "\n" +
- ex.getMessage());
+ "The Secondary Structure Prediction Service named "
+ + WebServiceName + " at " + WsURL
+ + " couldn't be located.", "Internal Jalview Error",
+ JOptionPane.WARNING_MESSAGE);
+ wsInfo.setProgressText("Serious! " + WebServiceName
+ + " Service location failed\nfor URL :" + WsURL + "\n"
+ + ex.getMessage());
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
}
return server;
}
-}
+ public void attachWSMenuEntry(JMenu wsmenu, final ServiceHandle sh,
+ final AlignFrame af)
+ {
+ final JMenuItem method = new JMenuItem(sh.getName());
+ method.setToolTipText(sh.getEndpointURL());
+ method.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ AlignmentView msa = af.gatherSeqOrMsaForSecStrPrediction();
+ if (msa.getSequences().length == 1)
+ {
+ // Single Sequence prediction
+ new jalview.ws.JPredClient(sh, af.getTitle(), false, msa, af,
+ true);
+ }
+ else
+ {
+ if (msa.getSequences().length > 1)
+ {
+ // Sequence profile based prediction
+ new jalview.ws.JPredClient(sh, af.getTitle(), true, msa, af,
+ true);
+ }
+ }
+ }
+ });
+ wsmenu.add(method);
+ }
+}
git://source.jalview.org / jalview.git / blobdiff