X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FJPredClient.java;h=3add58d8f47341ea3d6ce7e5a44e939b192d9dbf;hb=506d60f0e188723ddc91c26824b41ac7034df3fe;hp=e14816cf26ba77f76b5af84ac3fc3f621336f91d;hpb=60f2d6c034560415fd0139c8bc7df0c19cae1186;p=jalview.git diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java index e14816c..3add58d 100755 --- a/src/jalview/ws/JPredClient.java +++ b/src/jalview/ws/JPredClient.java @@ -1,17 +1,17 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) + * Copyright (C) 2008 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 @@ -30,20 +30,25 @@ 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); @@ -52,19 +57,27 @@ 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) @@ -92,7 +105,8 @@ 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(); @@ -103,7 +117,8 @@ 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++; } @@ -116,9 +131,9 @@ public class JPredClient if (msa && msf.length > 1) { - String altitle = getPredictionName(WebServiceName)+" 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++) @@ -126,7 +141,8 @@ 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. @@ -137,16 +153,13 @@ 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(); } @@ -154,31 +167,29 @@ 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 = getPredictionName(WebServiceName)+" 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(); } @@ -186,24 +197,27 @@ public class JPredClient private String getPredictionName(String webServiceName) { - if (webServiceName.toLowerCase().indexOf("secondary structure prediction")>-1) + if (webServiceName.toLowerCase().indexOf( + "secondary structure prediction") > -1) { return webServiceName; - } else { - return webServiceName+"secondary structure prediction"; + } + else + { + return webServiceName + "secondary structure prediction"; } } - public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI seq, - AlignFrame parentFrame) + 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); @@ -227,7 +241,7 @@ public class JPredClient } private void startJPredClient(String title, SequenceI[] msf, - AlignFrame parentFrame) + AlignFrame parentFrame) { if (wsInfo == null) { @@ -236,20 +250,26 @@ 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) @@ -257,27 +277,31 @@ 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) @@ -286,8 +310,7 @@ 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(); } @@ -296,14 +319,13 @@ 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; } @@ -314,23 +336,22 @@ 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); } @@ -338,7 +359,8 @@ public class JPredClient return server; } - public void attachWSMenuEntry(JMenu wsmenu, final ServiceHandle sh, final AlignFrame af) + public void attachWSMenuEntry(JMenu wsmenu, final ServiceHandle sh, + final AlignFrame af) { final JMenuItem method = new JMenuItem(sh.getName()); method.setToolTipText(sh.getEndpointURL()); @@ -350,15 +372,16 @@ public class JPredClient if (msa.getSequences().length == 1) { // Single Sequence prediction - new jalview.ws.JPredClient(sh, af.getTitle(), false, msa, af, true); + 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); + new jalview.ws.JPredClient(sh, af.getTitle(), true, msa, af, + true); } } }