/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.ws;\r
\r
-import ext.vamsas.*;\r
+import java.util.*;\r
\r
-import jalview.analysis.AlignSeq;\r
+import javax.swing.*;\r
\r
+import ext.vamsas.*;\r
+import jalview.analysis.*;\r
import jalview.datamodel.*;\r
-\r
import jalview.gui.*;\r
\r
-import org.apache.axis.client.*;\r
+public class JPredClient\r
+ extends WSClient\r
+{\r
+ ext.vamsas.JPredWS server;\r
+ String altitle = "";\r
+ java.util.Hashtable SequenceInfo = null;\r
\r
-import java.awt.*;\r
+ public JPredClient(String title, SequenceI[] msf)\r
+ {\r
+ wsInfo = setWebService();\r
\r
-import java.util.*;\r
+ SequenceI seq = msf[0];\r
+ altitle = "JNet prediction on " + seq.getName() +\r
+ " using alignment from " + title;\r
\r
-import javax.swing.*;\r
-\r
-import javax.xml.namespace.QName;\r
+ wsInfo.setProgressText("Job details for MSA based prediction (" +\r
+ title + ") on sequence :\n>" + seq.getName() + "\n" +\r
+ AlignSeq.extractGaps("-. ", seq.getSequence()) +\r
+ "\n");\r
\r
+ SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);\r
\r
-public class JPredClient extends WSClient {\r
- ext.vamsas.JPredWS server;\r
- String altitle = "";\r
- java.util.Hashtable SequenceInfo = null;\r
+ if (!locateWebService())\r
+ {\r
+ return;\r
+ }\r
\r
- public JPredClient(String title, SequenceI[] msf) {\r
- wsInfo = setWebService();\r
+ JPredThread jthread = new JPredThread(msf);\r
+ jthread.start();\r
+ }\r
+\r
+ public JPredClient(String title, SequenceI seq)\r
+ {\r
+ wsInfo = setWebService();\r
+ wsInfo.setProgressText("Job details for prediction on sequence :\n>" +\r
+ seq.getName() + "\n" +\r
+ AlignSeq.extractGaps("-. ", seq.getSequence()) +\r
+ "\n");\r
+ altitle = "JNet prediction for sequence " + seq.getName() + " from " +\r
+ title;\r
+\r
+ SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);\r
+\r
+ if (!locateWebService())\r
+ {\r
+ return;\r
+ }\r
\r
- SequenceI seq = msf[0];\r
- altitle = "JNet prediction on " + seq.getName() +\r
- " using alignment from " + title;\r
+ JPredThread jthread = new JPredThread(seq);\r
+ jthread.start();\r
+ }\r
+\r
+ private WebserviceInfo setWebService()\r
+ {\r
+ WebServiceName = "JNetWS";\r
+ WebServiceJobTitle = "JNet secondary structure prediction";\r
+ WebServiceReference =\r
+ "\"Cuff J. A and Barton G.J (1999) Application of enhanced " +\r
+ "multiple sequence alignment profiles to improve protein secondary structure prediction, " +\r
+ "Proteins 40:502-511\".";\r
+ WsURL = "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred";\r
+\r
+ WebserviceInfo wsInfo = new WebserviceInfo(WebServiceJobTitle,\r
+ WebServiceReference);\r
+\r
+ return wsInfo;\r
+ }\r
+\r
+ private boolean locateWebService()\r
+ {\r
+ JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default\r
+\r
+ try\r
+ {\r
+ this.server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set from properties\r
+ ( (JpredSoapBindingStub)this.server).setTimeout(60000); // one minute stub\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ JOptionPane.showMessageDialog(Desktop.desktop,\r
+ "The Secondary Structure Prediction Service named " +\r
+ WebServiceName + " at " + WsURL +\r
+ " couldn't be located.",\r
+ "Internal Jalview Error",\r
+ JOptionPane.WARNING_MESSAGE);\r
+ wsInfo.setProgressText("Serious! " + WebServiceName +\r
+ " Service location failed\nfor URL :" + WsURL +\r
+ "\n" +\r
+ ex.getMessage());\r
+ wsInfo.setStatus(wsInfo.STATE_STOPPED_SERVERERROR);\r
+\r
+ return false;\r
+ }\r
\r
- wsInfo.setProgressText("Job details for MSA based prediction (" +\r
- title + ") on sequence :\n>" + seq.getName() + "\n" +\r
- AlignSeq.extractGaps("-. ", seq.getSequence()) + "\n");\r
+ return true;\r
+ }\r
+\r
+ class JPredThread\r
+ extends Thread\r
+ {\r
+ String OutputHeader;\r
+ ext.vamsas.JpredResult result;\r
+ ext.vamsas.Sequence sequence;\r
+ ext.vamsas.Msfalignment msa;\r
+ String jobId;\r
+ boolean jobComplete = false;\r
+ int allowedServerExceptions = 3; // thread dies if too many exceptions.\r
+\r
+ JPredThread(SequenceI seq)\r
+ {\r
+ OutputHeader = wsInfo.getProgressText();\r
+ this.sequence = new ext.vamsas.Sequence();\r
+ this.sequence.setId(seq.getName());\r
+ this.sequence.setSeq(AlignSeq.extractGaps("-. ", seq.getSequence()));\r
+ }\r
\r
- SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);\r
+ JPredThread(SequenceI[] msf)\r
+ {\r
+ OutputHeader = wsInfo.getProgressText();\r
+ this.sequence = new ext.vamsas.Sequence();\r
+ this.sequence.setId(msf[0].getName());\r
+ this.sequence.setSeq(AlignSeq.extractGaps("-. ",\r
+ msf[0].getSequence()));\r
+\r
+ jalview.io.PileUpfile mwrite = new jalview.io.PileUpfile();\r
+ this.msa = new ext.vamsas.Msfalignment();\r
+ msa.setMsf(mwrite.print(msf));\r
+ }\r
\r
- if (!locateWebService()) {\r
- return;\r
+ public void run()\r
+ {\r
+ StartJob();\r
+\r
+ while (!jobComplete && (allowedServerExceptions > 0))\r
+ {\r
+ try\r
+ {\r
+ if ( (result = server.getresult(jobId)) == null)\r
+ {\r
+ throw (new Exception(\r
+ "Timed out when communicating with server\nTry again later.\n"));\r
+ }\r
+\r
+ if (result.isRunning())\r
+ {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);\r
+ }\r
+ else if (result.isQueued())\r
+ {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);\r
+ }\r
+\r
+ if (result.isFinished())\r
+ {\r
+ parseResult();\r
+ jobComplete = true;\r
+ jobsRunning--;\r
+ }\r
+ else\r
+ {\r
+ wsInfo.setProgressText(OutputHeader + "\n" +\r
+ result.getStatus());\r
+\r
+ if (! (result.isJobFailed() || result.isServerError()))\r
+ {\r
+ try\r
+ {\r
+ Thread.sleep(5000);\r
+ }\r
+ catch (InterruptedException ex1)\r
+ {\r
+ }\r
+\r
+ // System.out.println("I'm alive "+seqid+" "+jobid);\r
+ }\r
+ else\r
+ {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
+ }\r
+ }\r
}\r
-\r
- JPredThread jthread = new JPredThread(msf);\r
- jthread.start();\r
+ catch (Exception ex)\r
+ {\r
+ allowedServerExceptions--;\r
+ wsInfo.appendProgressText("\nJPredWS Server exception!\n" +\r
+ ex.getMessage());\r
+\r
+ try\r
+ {\r
+ if (allowedServerExceptions > 0)\r
+ {\r
+ Thread.sleep(5000);\r
+ }\r
+ }\r
+ catch (InterruptedException ex1)\r
+ {\r
+ }\r
+ }\r
+ }\r
+\r
+ if (! (result.isJobFailed() || result.isServerError()))\r
+ {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);\r
+ }\r
+ else\r
+ {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
+ }\r
}\r
\r
- public JPredClient(String title, SequenceI seq) {\r
- wsInfo = setWebService();\r
- wsInfo.setProgressText("Job details for prediction on sequence :\n>" +\r
- seq.getName() + "\n" +\r
- AlignSeq.extractGaps("-. ", seq.getSequence()) + "\n");\r
- altitle = "JNet prediction for sequence " + seq.getName() + " from " +\r
- title;\r
-\r
- SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);\r
-\r
- if (!locateWebService()) {\r
- return;\r
+ void StartJob()\r
+ {\r
+ try\r
+ {\r
+ if (msa != null)\r
+ {\r
+ jobId = server.predictOnMsa(msa);\r
+ }\r
+ else\r
+ {\r
+ jobId = server.predict(sequence);\r
}\r
\r
- JPredThread jthread = new JPredThread(seq);\r
- jthread.start();\r
+ if (jobId != null)\r
+ {\r
+ if (jobId.startsWith("Broken"))\r
+ {\r
+ throw new Exception("Submission " + jobId);\r
+ }\r
+ else\r
+ {\r
+ System.out.println(WsURL + " Job Id '" + jobId + "'");\r
+ }\r
+ }\r
+ else\r
+ {\r
+ throw new Exception("Server timed out - try again later\n");\r
+ }\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
+ allowedServerExceptions = 0;\r
+ jobComplete = false;\r
+\r
+ wsInfo.appendProgressText("Failed to submit the prediction.\n"\r
+ +\r
+ "It is most likely that there is a problem with the server.\n"\r
+ + "Just close the window\n");\r
+ System.err.println(\r
+ "JPredWS Client: Failed to submit the prediction (Probably a server error - see below)\n" +\r
+ e.toString() + "\n");\r
+\r
+ // e.printStackTrace(); TODO: JBPNote DEBUG\r
+ }\r
}\r
\r
- private WebserviceInfo setWebService() {\r
- WebServiceName = "JNetWS";\r
- WebServiceJobTitle = "JNet secondary structure prediction";\r
- WebServiceReference = "\"Cuff J. A and Barton G.J (1999) Application of enhanced " +\r
- "multiple sequence alignment profiles to improve protein secondary structure prediction, " +\r
- "Proteins 40:502-511\".";\r
- WsURL = "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred";\r
-\r
- WebserviceInfo wsInfo = new WebserviceInfo(WebServiceJobTitle,\r
- WebServiceReference);\r
-\r
- return wsInfo;\r
+ private void addFloatAnnotations(Alignment al, int[] gapmap,\r
+ Vector values, String Symname,\r
+ String Visname, float min,\r
+ float max, int winLength)\r
+ {\r
+ Annotation[] annotations = new Annotation[al.getWidth()];\r
+\r
+ for (int j = 0; j < values.size(); j++)\r
+ {\r
+ float value = Float.parseFloat(values.get(j).toString());\r
+ annotations[gapmap[j]] = new Annotation("", value + "", ' ',\r
+ value);\r
+ }\r
+\r
+ al.addAnnotation(new AlignmentAnnotation(Symname, Visname,\r
+ annotations, min, max, winLength));\r
}\r
\r
- private boolean locateWebService() {\r
- JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default\r
-\r
- try {\r
- this.server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set from properties\r
- ((JpredSoapBindingStub) this.server).setTimeout(60000); // one minute stub\r
- } catch (Exception ex) {\r
- JOptionPane.showMessageDialog(Desktop.desktop,\r
- "The Secondary Structure Prediction Service named " +\r
- WebServiceName + " at " + WsURL + " couldn't be located.",\r
- "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);\r
- wsInfo.setProgressText("Serious! " + WebServiceName +\r
- " Service location failed\nfor URL :" + WsURL + "\n" +\r
- ex.getMessage());\r
- wsInfo.setStatus(wsInfo.STATE_STOPPED_SERVERERROR);\r
-\r
- return false;\r
+ void parseResult()\r
+ {\r
+ // OutputHeader = output.getText();\r
+ if (result.isFailed())\r
+ {\r
+ OutputHeader += "Job failed.\n";\r
+ }\r
+\r
+ if (result.getStatus() != null)\r
+ {\r
+ OutputHeader += ("\n" + result.getStatus());\r
+ }\r
+\r
+ if (result.getPredfile() != null)\r
+ {\r
+ OutputHeader += ("\n" + result.getPredfile());\r
+\r
+ // JBPNote The returned files from a webservice could be hidden behind icons in the monitor window that, when clicked, pop up their corresponding data\r
+ }\r
+\r
+ if (result.getAligfile() != null)\r
+ {\r
+ OutputHeader += ("\n" + result.getAligfile());\r
+ }\r
+\r
+ wsInfo.setProgressText(OutputHeader);\r
+\r
+ try\r
+ {\r
+ // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File");\r
+ jalview.io.JPredFile prediction = new jalview.io.JPredFile(result.\r
+ getPredfile(),\r
+ "Paste");\r
+ SequenceI[] preds = prediction.getSeqsAsArray();\r
+ Alignment al;\r
+ int FirstSeq; // the position of the query sequence in Alignment al\r
+ boolean noMsa = true; // set if no MSA has been returned by JPred\r
+\r
+ if ( (this.msa != null) && (result.getAligfile() != null))\r
+ {\r
+ // we ignore the returned alignment if we only predicted on a single sequence\r
+ String format = jalview.io.IdentifyFile.Identify(result.getAligfile(),\r
+ "Paste");\r
+\r
+ if (jalview.io.FormatAdapter.formats.contains(format))\r
+ {\r
+ al = new Alignment(jalview.io.FormatAdapter.readFile(\r
+ result.getAligfile(), "Paste", format));\r
+ noMsa = false;\r
+ FirstSeq = 0;\r
+ }\r
+ else\r
+ {\r
+ throw (new Exception(\r
+ "Unknown format 'format' for file : \n" +\r
+ result.getAligfile()));\r
+ }\r
}\r
-\r
- return true;\r
- }\r
-\r
- class JPredThread extends Thread {\r
- String OutputHeader;\r
- ext.vamsas.JpredResult result;\r
- ext.vamsas.Sequence sequence;\r
- ext.vamsas.Msfalignment msa;\r
- String jobId;\r
- boolean jobComplete = false;\r
- int allowedServerExceptions = 3; // thread dies if too many exceptions.\r
-\r
- JPredThread(SequenceI seq) {\r
- OutputHeader = wsInfo.getProgressText();\r
- this.sequence = new ext.vamsas.Sequence();\r
- this.sequence.setId(seq.getName());\r
- this.sequence.setSeq(AlignSeq.extractGaps("-. ", seq.getSequence()));\r
+ else\r
+ {\r
+ al = new Alignment(preds);\r
+ FirstSeq = prediction.getQuerySeqPosition();\r
}\r
\r
- JPredThread(SequenceI[] msf) {\r
- OutputHeader = wsInfo.getProgressText();\r
- this.sequence = new ext.vamsas.Sequence();\r
- this.sequence.setId(msf[0].getName());\r
- this.sequence.setSeq(AlignSeq.extractGaps("-. ",\r
- msf[0].getSequence()));\r
+ if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(\r
+ al.getSequenceAt(FirstSeq), SequenceInfo))\r
+ {\r
+ throw (new Exception(\r
+ "Couldn't recover sequence properties for JNet Query sequence!"));\r
+ }\r
\r
- jalview.io.PileUpfile mwrite = new jalview.io.PileUpfile();\r
- this.msa = new ext.vamsas.Msfalignment();\r
- msa.setMsf(mwrite.print(msf));\r
+ AlignmentAnnotation annot;\r
+ Annotation[] annotations = null;\r
+ int i = 0;\r
+ int width = preds[0].getSequence().length();\r
+\r
+ int[] gapmap = al.getSequenceAt(FirstSeq).gapMap();\r
+\r
+ if (gapmap.length != width)\r
+ {\r
+ throw (new Exception(\r
+ "Jnet Client Error\nNumber of residues in supposed query sequence :\n" +\r
+ al.getSequenceAt(FirstSeq).getName() + "\n" +\r
+ al.getSequenceAt(FirstSeq).getSequence() +\r
+ "\nDiffer from number of prediction sites in \n" +\r
+ result.getPredfile() + "\n"));\r
}\r
\r
- public void run() {\r
- StartJob();\r
-\r
- while (!jobComplete && (allowedServerExceptions > 0)) {\r
- try {\r
- if ((result = server.getresult(jobId)) == null) {\r
- throw (new Exception(\r
- "Timed out when communicating with server\nTry again later.\n"));\r
- }\r
-\r
- if (result.isRunning()) {\r
- wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);\r
- } else if (result.isQueued()) {\r
- wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);\r
- }\r
-\r
- if (result.isFinished()) {\r
- parseResult();\r
- jobComplete = true;\r
- jobsRunning--;\r
- } else {\r
- wsInfo.setProgressText(OutputHeader + "\n" +\r
- result.getStatus());\r
-\r
- if (!(result.isJobFailed() || result.isServerError())) {\r
- try {\r
- Thread.sleep(5000);\r
- } catch (InterruptedException ex1) {\r
- }\r
-\r
- // System.out.println("I'm alive "+seqid+" "+jobid);\r
- } else {\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
- }\r
- }\r
- } catch (Exception ex) {\r
- allowedServerExceptions--;\r
- wsInfo.appendProgressText("\nJPredWS Server exception!\n" +\r
- ex.getMessage());\r
-\r
- try {\r
- if (allowedServerExceptions > 0) {\r
- Thread.sleep(5000);\r
- }\r
- } catch (InterruptedException ex1) {\r
- }\r
- }\r
+ // JBPNote Should also rename the query sequence sometime...\r
+ i = 0;\r
+\r
+ while (i < preds.length)\r
+ {\r
+ String id = preds[i].getName().toUpperCase();\r
+\r
+ if (id.startsWith("LUPAS") || id.startsWith("JNET") ||\r
+ id.startsWith("JPRED"))\r
+ {\r
+ annotations = new Annotation[al.getWidth()];\r
+\r
+ if (id.equals("JNETPRED") || id.equals("JNETPSSM") ||\r
+ id.equals("JNETFREQ") || id.equals("JNETHMM") ||\r
+ id.equals("JNETALIGN") || id.equals("JPRED"))\r
+ {\r
+ for (int j = 0; j < width; j++)\r
+ {\r
+ annotations[gapmap[j]] = new Annotation("", "",\r
+ preds[i].getCharAt(j), 0);\r
+ }\r
}\r
-\r
- if (!(result.isJobFailed() || result.isServerError())) {\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);\r
- } else {\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
+ else if (id.equals("JNETCONF"))\r
+ {\r
+ for (int j = 0; j < width; j++)\r
+ {\r
+ float value = Float.parseFloat(preds[i].getCharAt(\r
+ j) + "");\r
+ annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(\r
+ j) + "", "", preds[i].getCharAt(j),\r
+ value);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ for (int j = 0; j < width; j++)\r
+ {\r
+ annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(\r
+ j) + "", "", ' ', 0);\r
+ }\r
}\r
- }\r
\r
- void StartJob() {\r
- try {\r
- if (msa != null) {\r
- jobId = server.predictOnMsa(msa);\r
- } else {\r
- jobId = server.predict(sequence);\r
- }\r
-\r
- if (jobId != null) {\r
- if (jobId.startsWith("Broken")) {\r
- throw new Exception("Submission " + jobId);\r
- } else {\r
- System.out.println(WsURL + " Job Id '" + jobId + "'");\r
- }\r
- } else {\r
- throw new Exception("Server timed out - try again later\n");\r
- }\r
- } catch (Exception e) {\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
- allowedServerExceptions = 0;\r
- jobComplete = false;\r
-\r
- wsInfo.appendProgressText("Failed to submit the prediction.\n"\r
- +"It is most likely that there is a problem with the server.\n"\r
- +"Just close the window\n");\r
- System.err.println(\r
- "JPredWS Client: Failed to submit the prediction (Probably a server error - see below)\n" +\r
- e.toString() + "\n");\r
-\r
- // e.printStackTrace(); TODO: JBPNote DEBUG\r
+ if (id.equals("JNETCONF"))\r
+ {\r
+ annot = new AlignmentAnnotation(preds[i].getName(),\r
+ "JNet Output", annotations, 0f,\r
+ 10f, 1);\r
+ }\r
+ else\r
+ {\r
+ annot = new AlignmentAnnotation(preds[i].getName(),\r
+ "JNet Output", annotations);\r
}\r
- }\r
\r
- private void addFloatAnnotations(Alignment al, int[] gapmap,\r
- Vector values, String Symname, String Visname, float min,\r
- float max, int winLength) {\r
- Annotation[] annotations = new Annotation[al.getWidth()];\r
+ al.addAnnotation(annot);\r
\r
- for (int j = 0; j < values.size(); j++) {\r
- float value = Float.parseFloat(values.get(j).toString());\r
- annotations[gapmap[j]] = new Annotation("", value + "", ' ',\r
- value);\r
+ if (noMsa)\r
+ {\r
+ al.deleteSequence(preds[i]);\r
}\r
+ }\r
\r
- al.addAnnotation(new AlignmentAnnotation(Symname, Visname,\r
- annotations, min, max, winLength));\r
+ i++;\r
}\r
\r
- void parseResult() {\r
- // OutputHeader = output.getText();\r
- if (result.isFailed()) {\r
- OutputHeader += "Job failed.\n";\r
- }\r
-\r
- if (result.getStatus() != null) {\r
- OutputHeader += ("\n" + result.getStatus());\r
- }\r
+ Hashtable scores = prediction.getScores();\r
\r
- if (result.getPredfile() != null) {\r
- OutputHeader += ("\n" + result.getPredfile());\r
+ /* addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPH"),\r
+ "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);\r
\r
- // JBPNote The returned files from a webservice could be hidden behind icons in the monitor window that, when clicked, pop up their corresponding data\r
- }\r
+ addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPB"),\r
+ "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1);\r
\r
- if (result.getAligfile() != null) {\r
- OutputHeader += ("\n" + result.getAligfile());\r
- }\r
+ addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPC"),\r
+ "JnetpropC", "Jnet Coil Propensity", 0f,1f,1);\r
+ */\r
+ AlignFrame af = new AlignFrame(al);\r
\r
- wsInfo.setProgressText(OutputHeader);\r
-\r
- try {\r
- // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File");\r
- jalview.io.JPredFile prediction = new jalview.io.JPredFile(result.getPredfile(),\r
- "Paste");\r
- SequenceI[] preds = prediction.getSeqsAsArray();\r
- Alignment al;\r
- int FirstSeq; // the position of the query sequence in Alignment al\r
- boolean noMsa = true; // set if no MSA has been returned by JPred\r
-\r
- if ((this.msa != null) && (result.getAligfile() != null)) {\r
- // we ignore the returned alignment if we only predicted on a single sequence\r
- String format = jalview.io.IdentifyFile.Identify(result.getAligfile(),\r
- "Paste");\r
-\r
- if (jalview.io.FormatAdapter.formats.contains(format)) {\r
- al = new Alignment(jalview.io.FormatAdapter.readFile(\r
- result.getAligfile(), "Paste", format));\r
- noMsa = false;\r
- FirstSeq = 0;\r
- } else {\r
- throw (new Exception(\r
- "Unknown format 'format' for file : \n" +\r
- result.getAligfile()));\r
- }\r
- } else {\r
- al = new Alignment(preds);\r
- FirstSeq = prediction.getQuerySeqPosition();\r
- }\r
-\r
- if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(\r
- al.getSequenceAt(FirstSeq), SequenceInfo)) {\r
- throw (new Exception(\r
- "Couldn't recover sequence properties for JNet Query sequence!"));\r
- }\r
-\r
- AlignmentAnnotation annot;\r
- Annotation[] annotations = null;\r
- int i = 0;\r
- int width = preds[0].getSequence().length();\r
-\r
- int[] gapmap = al.getSequenceAt(FirstSeq).gapMap();\r
-\r
- if (gapmap.length != width) {\r
- throw (new Exception(\r
- "Jnet Client Error\nNumber of residues in supposed query sequence :\n" +\r
- al.getSequenceAt(FirstSeq).getName() + "\n" +\r
- al.getSequenceAt(FirstSeq).getSequence() +\r
- "\nDiffer from number of prediction sites in \n" +\r
- result.getPredfile() + "\n"));\r
- }\r
-\r
- // JBPNote Should also rename the query sequence sometime...\r
- i = 0;\r
-\r
- while (i < preds.length) {\r
- String id = preds[i].getName().toUpperCase();\r
-\r
- if (id.startsWith("LUPAS") || id.startsWith("JNET") ||\r
- id.startsWith("JPRED")) {\r
- annotations = new Annotation[al.getWidth()];\r
-\r
- if (id.equals("JNETPRED") || id.equals("JNETPSSM") ||\r
- id.equals("JNETFREQ") || id.equals("JNETHMM") ||\r
- id.equals("JNETALIGN") || id.equals("JPRED")) {\r
- for (int j = 0; j < width; j++) {\r
- annotations[gapmap[j]] = new Annotation("", "",\r
- preds[i].getCharAt(j), 0);\r
- }\r
- } else if (id.equals("JNETCONF")) {\r
- for (int j = 0; j < width; j++) {\r
- float value = Float.parseFloat(preds[i].getCharAt(\r
- j) + "");\r
- annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(\r
- j) + "", "", preds[i].getCharAt(j),\r
- value);\r
- }\r
- } else {\r
- for (int j = 0; j < width; j++) {\r
- annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(\r
- j) + "", "", ' ', 0);\r
- }\r
- }\r
-\r
- if (id.equals("JNETCONF")) {\r
- annot = new AlignmentAnnotation(preds[i].getName(),\r
- "JNet Output", annotations, 0f, 10f, 1);\r
- }\r
- else {\r
- annot = new AlignmentAnnotation(preds[i].getName(),\r
- "JNet Output", annotations);\r
- }\r
-\r
- al.addAnnotation(annot);\r
-\r
- if (noMsa) {\r
- al.deleteSequence(preds[i]);\r
- }\r
- }\r
-\r
- i++;\r
- }\r
-\r
- Hashtable scores = prediction.getScores();\r
-\r
- /* addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPH"),\r
- "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);\r
-\r
- addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPB"),\r
- "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1);\r
-\r
- addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPC"),\r
- "JnetpropC", "Jnet Coil Propensity", 0f,1f,1);\r
- */\r
- AlignFrame af = new AlignFrame(al);\r
-\r
- Desktop.addInternalFrame(af, altitle,\r
- AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);\r
- } catch (Exception ex) {\r
- ex.printStackTrace();\r
- }\r
- }\r
+ Desktop.addInternalFrame(af, altitle,\r
+ AlignFrame.NEW_WINDOW_WIDTH,\r
+ AlignFrame.NEW_WINDOW_HEIGHT);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
}\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff