+++ /dev/null
-/*
- * 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 ext.vamsas.*;
-import jalview.analysis.*;
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-
-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)
- {
- super();
- 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
- */
- private void startJPredClient(String title, boolean msa,
- jalview.datamodel.AlignmentView alview, AlignFrame parentFrame,
- boolean viewonly)
- {
- AlignmentView input = alview;
- if (wsInfo == null)
- {
- wsInfo = setWebService();
- }
- Jpred server = locateWebService();
- if (server == null)
- {
- Cache.log.warn("Couldn't find a Jpred webservice to invoke!");
- return;
- }
- 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)
- {
- 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 gapMap[] = seq.gapMap();
- for (int contig = 0; contig < viscontigs.length; contig += 2)
- {
-
- while (spos < gapMap.length && gapMap[spos] < viscontigs[contig])
- {
- spos++;
- }
- 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;
- }
- }
- if (msa && msf.length > 1)
- {
-
- 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)
- {
- // 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.getSequenceAsString())
- + "\n");
- JPredThread jthread = new JPredThread(wsInfo, altitle, server,
- 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 = getPredictionName(WebServiceName) + " for "
- + (viewonly ? "visible " : "") + "sequence " + seq.getName()
- + " from " + title;
- String seqname = seq.getName();
- 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.getSequenceAsString())
- + "\n");
- JPredThread jthread = new JPredThread(wsInfo, altitle, server, WsURL,
- SequenceInfo, seq, delMap, alview, parentFrame);
- wsInfo.setthisService(jthread);
- jthread.start();
- }
- }
-
- 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)
- {
- wsInfo = setWebService(sh);
- startJPredClient(title, msa, parentFrame);
- }
-
- public JPredClient(String title, SequenceI[] msf)
- {
- startJPredClient(title, msf, null);
- }
-
- public JPredClient(String title, SequenceI seq)
- {
- startJPredClient(title, seq, null);
- }
-
- public JPredClient()
- {
-
- super();
- // add a class reference to the list
- }
-
- private void startJPredClient(String title, SequenceI[] msf,
- AlignFrame parentFrame)
- {
- if (wsInfo == null)
- {
- wsInfo = setWebService();
- }
-
- SequenceI seq = msf[0];
-
- 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.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);
-
- Jpred server = locateWebService();
- if (server == null)
- {
- return;
- }
-
- 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)
- {
- if (wsInfo == null)
- {
- wsInfo = setWebService();
- }
- 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);
-
- Jpred server = locateWebService();
- if (server == null)
- {
- return;
- }
-
- JPredThread jthread = new JPredThread(wsInfo, altitle, server, WsURL,
- SequenceInfo, seq, null, null, parentFrame);
- wsInfo.setthisService(jthread);
- jthread.start();
- }
-
- private WebserviceInfo setWebService()
- {
- 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\".";
- WsURL = "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred";
-
- WebserviceInfo wsInfo = new WebserviceInfo(WebServiceJobTitle,
- WebServiceReference);
-
- return wsInfo;
- }
-
- private ext.vamsas.Jpred locateWebService()
- {
- ext.vamsas.JpredServiceLocator loc = new JpredServiceLocator(); // Default
- 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);
-
- } 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());
- 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