X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FJPredClient.java;h=bb691dc615f9229ba4096636845b1f4094fb3feb;hb=d423f22792e47dbc800ae220a58677f988971d06;hp=2475fb1ec6ddd587c8ff1d1fab5ee4f07f0f3405;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java index 2475fb1..bb691dc 100755 --- a/src/jalview/ws/JPredClient.java +++ b/src/jalview/ws/JPredClient.java @@ -1,23 +1,24 @@ /* - * 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 . */ package jalview.ws; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; import java.util.*; import javax.swing.*; @@ -28,20 +29,25 @@ import jalview.bin.*; import jalview.datamodel.*; import jalview.gui.*; -public class JPredClient - extends WSClient +public class JPredClient extends WSClient { /** * 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 + * + * @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) + public JPredClient(ext.vamsas.ServiceHandle sh, String title, + boolean msa, AlignmentView alview, AlignFrame parentFrame, + boolean viewonly) { super(); wsInfo = setWebService(sh); @@ -50,19 +56,27 @@ public class JPredClient } /** - * 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) @@ -90,7 +104,8 @@ public class JPredClient 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 + // 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(); @@ -101,7 +116,8 @@ public class JPredClient { spos++; } - while (spos < gapMap.length && gapMap[spos] <= viscontigs[contig + 1]) + while (spos < gapMap.length + && gapMap[spos] <= viscontigs[contig + 1]) { delMap[i++] = spos++; } @@ -114,9 +130,9 @@ public class JPredClient 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++) @@ -124,7 +140,8 @@ public class JPredClient aln[i] = msf[i].getSeq('-'); } - Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, true); + Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, + true); if (viewonly) { // Remove hidden regions from sequence objects. @@ -135,16 +152,13 @@ public class JPredClient } 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"); + 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(); } @@ -152,45 +166,57 @@ public class JPredClient { if (!msa && msf.length > 1) { - throw new Error("Implementation Error! Multiple single sequence prediction jobs are not yet supported."); + 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; + + String altitle = getPredictionName(WebServiceName) + " for " + + (viewonly ? "visible " : "") + "sequence " + seq.getName() + + " from " + title; String seqname = seq.getName(); - Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash( - seq); + 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"); + 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); @@ -206,8 +232,15 @@ public class JPredClient startJPredClient(title, seq, null); } + public JPredClient() + { + + super(); + // add a class reference to the list + } + private void startJPredClient(String title, SequenceI[] msf, - AlignFrame parentFrame) + AlignFrame parentFrame) { if (wsInfo == null) { @@ -216,20 +249,26 @@ public class JPredClient 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"); + 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); + Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, + true); Jpred server = locateWebService(); if (server == null) @@ -237,27 +276,31 @@ public class JPredClient 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) + 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); + 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) @@ -266,8 +309,7 @@ public class JPredClient } JPredThread jthread = new JPredThread(wsInfo, altitle, server, WsURL, - SequenceInfo, seq, null, null, - parentFrame); + SequenceInfo, seq, null, null, parentFrame); wsInfo.setthisService(jthread); jthread.start(); } @@ -276,14 +318,13 @@ public class JPredClient { 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; } @@ -294,27 +335,56 @@ public class JPredClient 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); + } }