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From: Stefan K. <sh...@us...> - 2006-06-19 13:04:30
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/tests In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv20483/src/java/org/openscience/nmrshiftdb/tests Modified Files: NMRShiftDBServicesTest.java Log Message: rounding in spectrum Index: NMRShiftDBServicesTest.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/tests/NMRShiftDBServicesTest.java,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -r1.4 -r1.5 *** NMRShiftDBServicesTest.java 14 Jun 2006 20:42:17 -0000 1.4 --- NMRShiftDBServicesTest.java 19 Jun 2006 13:04:20 -0000 1.5 *************** *** 1,9 **** package org.openscience.nmrshiftdb.tests; - import java.io.File; import java.io.InputStream; import java.net.URL; import java.util.Vector; import javax.xml.parsers.DocumentBuilder; import javax.xml.parsers.DocumentBuilderFactory; --- 1,9 ---- package org.openscience.nmrshiftdb.tests; import java.io.InputStream; import java.net.URL; import java.util.Vector; + import javax.xml.namespace.QName; import javax.xml.parsers.DocumentBuilder; import javax.xml.parsers.DocumentBuilderFactory; *************** *** 16,23 **** import org.apache.axis.utils.Options; import org.apache.axis.utils.XMLUtils; - import org.apache.turbine.om.NumberKey; - import org.openscience.nmrshiftdb.om.DBMolecule; - import org.openscience.nmrshiftdb.om.DBSpectrum; - import org.openscience.nmrshiftdb.om.DBSpectrumPeer; import org.w3c.dom.Document; import org.w3c.dom.Element; --- 16,19 ---- *************** *** 26,30 **** public class NMRShiftDBServicesTest extends TestCase { ! String server="almost.cubic.uni-koeln.de"; public NMRShiftDBServicesTest(String text){ --- 22,26 ---- public class NMRShiftDBServicesTest extends TestCase { ! String server="127.0.0.1:8080"; public NMRShiftDBServicesTest(String text){ *************** *** 75,78 **** --- 71,75 ---- Service service = new Service(); Call call = (Call) service.createCall(); + call.setOperationName("getSpectrumTypes"); call.setTargetEndpointAddress( new URL(opts.getURL()) ); DocumentBuilder builder; *************** *** 82,85 **** --- 79,94 ---- Element cdataElem; cdataElem = doc.createElementNS("http://www.nmrshiftdb.org/ws/NMRShiftDB/", "getSpectrumTypes"); + Element reqElem; + reqElem = doc.createElementNS("http://www.nmrshiftdb.org/ws/NMRShiftDB/", "spectrumTypeName"); + Node node; + node = doc.createTextNode("13C"); + reqElem.appendChild(node); + String filename = "org/openscience/nmrshiftdb/tests/butadiene.cml"; + InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); + + Document document = builder.parse(ins); + Node nodeimp=doc.importNode(document.getChildNodes().item(0),true); + cdataElem.appendChild(nodeimp); + cdataElem.appendChild(reqElem); input[0] = new SOAPBodyElement(cdataElem); System.out.println(input[0].toString()); |
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From: Stefan K. <sh...@us...> - 2006-06-19 13:04:27
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv20483/src/java/org/openscience/nmrshiftdb/portlets Modified Files: PredictPortlet.java Log Message: rounding in spectrum Index: PredictPortlet.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets/PredictPortlet.java,v retrieving revision 1.160 retrieving revision 1.161 diff -C2 -r1.160 -r1.161 *** PredictPortlet.java 1 Jun 2006 14:47:14 -0000 1.160 --- PredictPortlet.java 19 Jun 2006 13:04:20 -0000 1.161 *************** *** 17,20 **** --- 17,21 ---- import java.sql.ResultSetMetaData; import java.sql.Statement; + import java.text.DecimalFormat; import java.util.Collections; import java.util.HashMap; *************** *** 118,122 **** */ public static VelocityContext getContext(HttpSession session, boolean calculated, boolean measured, StringBuffer messages, Object servconorrundata, HttpServletRequest request, boolean print) throws IOException, FileNotFoundException, Exception { ! VelocityContext context = new VelocityContext(); ServletConfig servcon; if (servconorrundata instanceof RunData) { --- 119,124 ---- */ public static VelocityContext getContext(HttpSession session, boolean calculated, boolean measured, StringBuffer messages, Object servconorrundata, HttpServletRequest request, boolean print) throws IOException, FileNotFoundException, Exception { ! DecimalFormat myFormatter = new DecimalFormat("###.##"); ! VelocityContext context = new VelocityContext(); ServletConfig servcon; if (servconorrundata instanceof RunData) { *************** *** 458,462 **** if(predictbyhose){ double[] statisticshose = AtomUtils.predictRange(mol, mol.getAtomAt(l), calculated, measured, null, comment, true, false, null, predictionValuesForAppletMap, ((Integer) session.getAttribute("choosennumber")).intValue(), true, hoseCodePrediction, ((Boolean)session.getAttribute("trueonly")).booleanValue()); ! comments[l].append("; HOSE code: "+((Math.floor(statisticshose[1] * 100)) / 100)+" with code "+hoseCodePrediction); }else{ alreadyDone[mothernumber]=true; --- 460,464 ---- if(predictbyhose){ double[] statisticshose = AtomUtils.predictRange(mol, mol.getAtomAt(l), calculated, measured, null, comment, true, false, null, predictionValuesForAppletMap, ((Integer) session.getAttribute("choosennumber")).intValue(), true, hoseCodePrediction, ((Boolean)session.getAttribute("trueonly")).booleanValue()); ! comments[l].append("; HOSE code: "+myFormatter.format(statisticshose[1])+" with code "+hoseCodePrediction); }else{ alreadyDone[mothernumber]=true; *************** *** 488,492 **** if(predictbyhose){ double[] statisticshose = AtomUtils.predictRange(mol, mol.getAtomAt(l), calculated, measured, null, comment, true, false, null, predictionValuesForAppletMap, ((Integer) session.getAttribute("choosennumber")).intValue(), true, hoseCodePrediction, ((Boolean)session.getAttribute("trueonly")).booleanValue()); ! comments[l].append("; HOSE code: "+((Math.floor(statisticshose[1] * 100)) / 100)+" with code "+hoseCodePrediction); } ((ValuesForVelocityBean) elementsOfChoosenType.get(elementsOfChoosenType.size() - 1)).statistics = statistics; --- 490,494 ---- if(predictbyhose){ double[] statisticshose = AtomUtils.predictRange(mol, mol.getAtomAt(l), calculated, measured, null, comment, true, false, null, predictionValuesForAppletMap, ((Integer) session.getAttribute("choosennumber")).intValue(), true, hoseCodePrediction, ((Boolean)session.getAttribute("trueonly")).booleanValue()); ! comments[l].append("; HOSE code: "+myFormatter.format(statisticshose[1])+" with code "+hoseCodePrediction); } ((ValuesForVelocityBean) elementsOfChoosenType.get(elementsOfChoosenType.size() - 1)).statistics = statistics; *************** *** 528,536 **** for (int k = 0; k < it.atoms.size(); k++) { if (session.getAttribute("applet") != null && session.getAttribute("applet").equals("applet")) { ! spectrumForApplet.append("S(0,"+it.sortPosition+","+ (((Float) it.atoms.get(k)).intValue()+1) +(predictAtomType.equals("C") ? ","+it.multiplicityString : "")+")="+((Math.floor(it.value1 * 100)) / 100)+"|"); }else{ ! spectrumForApplet.append(((Math.floor(it.value1 * 100)) / 100) + (predictAtomType.equals("C") ? it.multiplicityString : "") + ";" + it.value2 + ";" + ((Float) it.atoms.get(k)).intValue() + "|"); } ! tooltips.append((((Float) it.atoms.get(k)).intValue()+1)+"|"+ ((Math.floor(it.value1 * 100)) / 100) +"|"); } } --- 530,538 ---- for (int k = 0; k < it.atoms.size(); k++) { if (session.getAttribute("applet") != null && session.getAttribute("applet").equals("applet")) { ! spectrumForApplet.append("S(0,"+it.sortPosition+","+ (((Float) it.atoms.get(k)).intValue()+1) +(predictAtomType.equals("C") ? ","+it.multiplicityString : "")+")="+myFormatter.format(it.value1 * 100)+"|"); }else{ ! spectrumForApplet.append((myFormatter.format(it.value1) + (predictAtomType.equals("C") ? it.multiplicityString : "") + ";" + it.value2 + ";" + ((Float) it.atoms.get(k)).intValue() + "|"); } ! tooltips.append((((Float) it.atoms.get(k)).intValue()+1)+"|"+ myFormatter.format(it.value1) +"|"); } } *************** *** 546,552 **** double[] values = (double[]) predictionValuesForAppletMap.get(thisPrediction); if (values != null) { ! predictionValuesForApplet.append(((Math.floor(thisPrediction.doubleValue() * 100)) / 100) + "|"); for (int k = 0; k < values.length; k++) { ! predictionValuesForApplet.append(((Math.floor(values[k] * 100)) / 100) + ";"); } predictionValuesForApplet.append("|"); --- 548,554 ---- double[] values = (double[]) predictionValuesForAppletMap.get(thisPrediction); if (values != null) { ! predictionValuesForApplet.append(myFormatter.format(thisPrediction.doubleValue()) + "|"); for (int k = 0; k < values.length; k++) { ! predictionValuesForApplet.append(myFormatter.format(values[k]) + ";"); } predictionValuesForApplet.append("|"); |
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From: Stefan K. <sh...@us...> - 2006-06-14 20:42:28
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/deploymentdescriptors In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv22967/src/deploymentdescriptors Modified Files: NMRShiftDB.wsdd NMRShiftDB.wsdl Log Message: started a getSpectrumTypes webservice Index: NMRShiftDB.wsdd =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/deploymentdescriptors/NMRShiftDB.wsdd,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -r1.1 -r1.2 *** NMRShiftDB.wsdd 7 Jun 2006 19:13:49 -0000 1.1 --- NMRShiftDB.wsdd 14 Jun 2006 20:42:17 -0000 1.2 *************** *** 14,18 **** <!-- End of the definitions for the SOAPMonitor --> <parameter name="className" ! value="test.NMRShiftDBServiceBindingImpl"/> <parameter name="allowedMethods" value="*"/> <wsdlFile>NMRShiftDB.wsdl</wsdlFile> --- 14,18 ---- <!-- End of the definitions for the SOAPMonitor --> <parameter name="className" ! value="org.openscience.nmrshiftdb.webservices.NMRShiftDBServiceBindingImpl"/> <parameter name="allowedMethods" value="*"/> <wsdlFile>NMRShiftDB.wsdl</wsdlFile> Index: NMRShiftDB.wsdl =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/deploymentdescriptors/NMRShiftDB.wsdl,v retrieving revision 1.5 retrieving revision 1.6 diff -C2 -r1.5 -r1.6 *** NMRShiftDB.wsdl 13 Jun 2006 20:42:22 -0000 1.5 --- NMRShiftDB.wsdl 14 Jun 2006 20:42:17 -0000 1.6 *************** *** 49,52 **** --- 49,57 ---- name="doPredictionRequest" /> </wsdl:message> + <wsdl:message name="getSpectrumTypesResponse"> + <wsdl:part + type="xsd:string" + name="getSpectrumTypesResponse" /> + </wsdl:message> <wsdl:portType name="NMRShiftDB"> <wsdl:operation name="doPrediction"> *************** *** 54,57 **** --- 59,65 ---- <wsdl:output message="tns:doPredictionResponse" /> </wsdl:operation> + <wsdl:operation name="getSpectrumTypes"> + <wsdl:output message="tns:getSpectrumTypesResponse" /> + </wsdl:operation> </wsdl:portType> <wsdl:binding *************** *** 70,73 **** --- 78,90 ---- </wsdl:output> </wsdl:operation> + <wsdl:operation name="getSpectrumTypes"> + <soap:operation soapAction="http://www.nmrshiftdb.org/axis/services/NMRShiftDB?method=getSpectrumTypes" /> + <wsdl:input> + <soap:body use="literal" /> + </wsdl:input> + <wsdl:output> + <soap:body use="literal" /> + </wsdl:output> + </wsdl:operation> </wsdl:binding> <wsdl:service name="NMRShiftDB"> |
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From: Stefan K. <sh...@us...> - 2006-06-14 20:42:26
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv22967/src/java/org/openscience/nmrshiftdb/webservices Modified Files: NMRShiftDBServiceBindingImpl.java Log Message: started a getSpectrumTypes webservice Index: NMRShiftDBServiceBindingImpl.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices/NMRShiftDBServiceBindingImpl.java,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -r1.3 -r1.4 *** NMRShiftDBServiceBindingImpl.java 12 Jun 2006 13:57:22 -0000 1.3 --- NMRShiftDBServiceBindingImpl.java 14 Jun 2006 20:42:17 -0000 1.4 *************** *** 2,7 **** --- 2,11 ---- import java.io.ByteArrayInputStream; + import java.io.File; + import java.io.FileInputStream; import java.rmi.RemoteException; import java.util.HashMap; + import java.util.Properties; + import java.util.Vector; import javax.xml.parsers.DocumentBuilder; *************** *** 13,16 **** --- 17,21 ---- import org.apache.turbine.util.TurbineConfig; + import org.apache.turbine.util.db.Criteria; import org.openscience.cdk.ChemFile; import org.openscience.cdk.interfaces.IChemFile; *************** *** 18,23 **** --- 23,30 ---- import org.openscience.cdk.io.CMLReader; import org.openscience.nmrshiftdb.PredictionTool; + import org.openscience.nmrshiftdb.om.DBSpectrum; import org.openscience.nmrshiftdb.om.DBSpectrumType; import org.openscience.nmrshiftdb.om.DBSpectrumTypePeer; + import org.openscience.nmrshiftdb.util.GeneralUtils; import org.xmlcml.cml.element.CMLPeak; import org.xmlcml.cml.element.CMLPeakList; *************** *** 25,30 **** --- 32,40 ---- public class NMRShiftDBServiceBindingImpl implements NMRShiftDB { + + private final static String webinfdir="/usr/local/jakarta-tomcat-3.3.2/webapps/jetspeed/WEB-INF/"; public org.w3c.dom.Document doPrediction(org.w3c.dom.Document request) throws RemoteException { + System.err.println("lkj2222"); org.w3c.dom.Document document = null; try{ *************** *** 36,40 **** cfile=(IChemFile)cmlreader.read(cfile); IMolecule mol=cfile.getChemSequence(0).getChemModel(0).getSetOfMolecules().getMolecule(0); ! TurbineConfig tc = new TurbineConfig("", "/usr/local/jakarta-tomcat-3.3.2/webapps/jetspeed/WEB-INF/conf/TurbineResources.properties"); tc.init(); String spectype=eltype.getChild(0).getValue(); --- 46,55 ---- cfile=(IChemFile)cmlreader.read(cfile); IMolecule mol=cfile.getChemSequence(0).getChemModel(0).getSetOfMolecules().getMolecule(0); ! TurbineConfig tc = new TurbineConfig("", webinfdir+"conf/TurbineResources.properties"); ! File nmrpropsFile = new File(webinfdir+"conf/NMRShiftDB.properties"); ! Properties nmrprops = new Properties(); ! nmrprops.load(new FileInputStream(nmrpropsFile)); ! GeneralUtils.nmrprops=nmrprops; ! GeneralUtils.logToSql("Prediction WebService - " + elmol.toXML(), null); tc.init(); String spectype=eltype.getChild(0).getValue(); *************** *** 43,47 **** dbspectype=DBSpectrumTypePeer.getByName(spectype); CMLSpectrum spectrum=new CMLSpectrum(); ! spectrum.setNamespaceURI("http://www.xml-cml.org/schema/cml2/spect"); CMLPeakList peakList=new CMLPeakList(); spectrum.addPeakList(peakList); --- 58,62 ---- dbspectype=DBSpectrumTypePeer.getByName(spectype); CMLSpectrum spectrum=new CMLSpectrum(); ! //spectrum.setNamespaceURI("http://www.xml-cml.org/schema/cml2/spect"); CMLPeakList peakList=new CMLPeakList(); spectrum.addPeakList(peakList); *************** *** 67,69 **** --- 82,99 ---- } + public String getSpectrumTypes() throws RemoteException { + System.err.println("lkj"); + StringBuffer sb=new StringBuffer(); + try{ + TurbineConfig tc = new TurbineConfig("", webinfdir+"conf/TurbineResources.properties"); + tc.init(); + Vector v=DBSpectrumTypePeer.doSelect(new Criteria()); + for(int i=0;i<v.size();i++){ + sb.append(((DBSpectrumType)v.get(i)).getName()+" "); + } + }catch(Exception ex){ + throw new RemoteException(ex.getMessage(),ex); + } + return sb.toString().trim(); + } } |
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From: Stefan K. <sh...@us...> - 2006-06-14 20:42:25
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/tests In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv22967/src/java/org/openscience/nmrshiftdb/tests Modified Files: NMRShiftDBServicesTest.java Log Message: started a getSpectrumTypes webservice Index: NMRShiftDBServicesTest.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/tests/NMRShiftDBServicesTest.java,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -r1.3 -r1.4 *** NMRShiftDBServicesTest.java 12 Jun 2006 13:57:22 -0000 1.3 --- NMRShiftDBServicesTest.java 14 Jun 2006 20:42:17 -0000 1.4 *************** *** 69,72 **** assertEquals(1,e.getChildNodes().getLength()); } ! } --- 69,96 ---- assertEquals(1,e.getChildNodes().getLength()); } ! public void testGetSpectrumTypes() throws Exception{ ! Options opts = new Options(new String[0]); ! // Modify it to the location of your service ! opts.setDefaultURL("http://"+server+"/axis/services/NMRShiftDB"); ! Service service = new Service(); ! Call call = (Call) service.createCall(); ! call.setTargetEndpointAddress( new URL(opts.getURL()) ); ! DocumentBuilder builder; ! builder = DocumentBuilderFactory.newInstance().newDocumentBuilder(); ! SOAPBodyElement[] input = new SOAPBodyElement[1]; ! Document doc = builder.newDocument(); ! Element cdataElem; ! cdataElem = doc.createElementNS("http://www.nmrshiftdb.org/ws/NMRShiftDB/", "getSpectrumTypes"); ! input[0] = new SOAPBodyElement(cdataElem); ! System.out.println(input[0].toString()); ! ! ! Vector elems = (Vector) call.invoke( input ); ! SOAPBodyElement elem = null ; ! Element e = null ; ! elem = (SOAPBodyElement) elems.get(0); ! e = elem.getAsDOM(); ! System.err.println(XMLUtils.ElementToString(e)); ! assertEquals(1,e.getChildNodes().getLength()); ! } } |
Update of /cvsroot/nmrshiftdb/nmrshiftdb/lib In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv16050/lib Modified Files: cdk-builder3d.jar cdk-charges.jar cdk-core.jar cdk-data.jar cdk-extra.jar cdk-forcefield.jar cdk-interfaces.jar cdk-io.jar cdk-libio-cml.jar cdk-pdb-cml.jar cdk-pdb.jar cdk-qsar-cml.jar cdk-qsar.jar cdk-render.jar cdk-smiles.jar cdk-standard.jar cdk-valencycheck.jar Log Message: new cdk/jcp Index: cdk-builder3d.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-builder3d.jar,v retrieving revision 1.48 retrieving revision 1.49 diff -C2 -r1.48 -r1.49 Binary files /tmp/cvsKpFYms and /tmp/cvs2tYm1d differ Index: cdk-charges.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-charges.jar,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -r1.3 -r1.4 Binary files /tmp/cvstNN6RG and /tmp/cvstd1nKs differ Index: cdk-core.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-core.jar,v retrieving revision 1.120 retrieving revision 1.121 diff -C2 -r1.120 -r1.121 Binary files /tmp/cvsfE8PJF and /tmp/cvs5A4mEr differ Index: cdk-data.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-data.jar,v retrieving revision 1.44 retrieving revision 1.45 diff -C2 -r1.44 -r1.45 Binary files /tmp/cvsSaFh5G and /tmp/cvsKxc41s differ Index: cdk-extra.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-extra.jar,v retrieving revision 1.158 retrieving revision 1.159 diff -C2 -r1.158 -r1.159 Binary files /tmp/cvs7aRT5K and /tmp/cvsaKPm7w differ Index: cdk-forcefield.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-forcefield.jar,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -r1.3 -r1.4 Binary files /tmp/cvsPpKrVN and /tmp/cvs8O86Zz differ Index: cdk-interfaces.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-interfaces.jar,v retrieving revision 1.36 retrieving revision 1.37 diff -C2 -r1.36 -r1.37 Binary files /tmp/cvsEN8wqP and /tmp/cvsS7VlxB differ Index: cdk-io.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-io.jar,v retrieving revision 1.110 retrieving revision 1.111 diff -C2 -r1.110 -r1.111 Binary files /tmp/cvsJAXOhO and /tmp/cvsCAOzsA differ Index: cdk-libio-cml.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-libio-cml.jar,v retrieving revision 1.36 retrieving revision 1.37 diff -C2 -r1.36 -r1.37 Binary files /tmp/cvsc5BQnU and /tmp/cvs3U9UCG differ Index: cdk-pdb-cml.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-pdb-cml.jar,v retrieving revision 1.36 retrieving revision 1.37 diff -C2 -r1.36 -r1.37 Binary files /tmp/cvsyUDAjT and /tmp/cvsl34qAF differ Index: cdk-pdb.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-pdb.jar,v retrieving revision 1.36 retrieving revision 1.37 diff -C2 -r1.36 -r1.37 Binary files /tmp/cvsZidCIW and /tmp/cvsA2Mi1I differ Index: cdk-qsar-cml.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-qsar-cml.jar,v retrieving revision 1.36 retrieving revision 1.37 diff -C2 -r1.36 -r1.37 Binary files /tmp/cvsOxx4GX and /tmp/cvscVdy1J differ Index: cdk-qsar.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-qsar.jar,v retrieving revision 1.51 retrieving revision 1.52 diff -C2 -r1.51 -r1.52 Binary files /tmp/cvso32rAW and /tmp/cvs5cODXI differ Index: cdk-render.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-render.jar,v retrieving revision 1.91 retrieving revision 1.92 diff -C2 -r1.91 -r1.92 Binary files /tmp/cvsUHHLCY and /tmp/cvsbDqR2K differ Index: cdk-smiles.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-smiles.jar,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -r1.6 -r1.7 Binary files /tmp/cvsi3reb2 and /tmp/cvsdOBfDO differ Index: cdk-standard.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-standard.jar,v retrieving revision 1.105 retrieving revision 1.106 diff -C2 -r1.105 -r1.106 Binary files /tmp/cvscubN80 and /tmp/cvsqFDsDN differ Index: cdk-valencycheck.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-valencycheck.jar,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -r1.6 -r1.7 Binary files /tmp/cvs4kljF2 and /tmp/cvs417YbP differ |
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From: Stefan K. <sh...@us...> - 2006-06-13 20:42:56
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/deploymentdescriptors In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv16050/src/deploymentdescriptors Modified Files: NMRShiftDB.wsdl Log Message: new cdk/jcp Index: NMRShiftDB.wsdl =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/deploymentdescriptors/NMRShiftDB.wsdl,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -r1.4 -r1.5 *** NMRShiftDB.wsdl 12 Jun 2006 11:27:28 -0000 1.4 --- NMRShiftDB.wsdl 13 Jun 2006 20:42:22 -0000 1.5 *************** *** 5,10 **** xmlns:wsdl="http://schemas.xmlsoap.org/wsdl/" xmlns:xsd="http://www.w3.org/2001/XMLSchema" ! xmlns:cml="http://www.xml-cml.org/schema/cml2/core" ! Â xmlns:soapenc="http://schemas.xmlsoap.org/soap/encoding/" name="NMRShiftDB" targetNamespace="http://www.nmrshiftdb.org/ws/NMRShiftDB/"> --- 5,10 ---- xmlns:wsdl="http://schemas.xmlsoap.org/wsdl/" xmlns:xsd="http://www.w3.org/2001/XMLSchema" ! xmlns:cml="http://www.xml-cml.org/schema" ! xmlns:soapenc="http://schemas.xmlsoap.org/soap/encoding/" name="NMRShiftDB" targetNamespace="http://www.nmrshiftdb.org/ws/NMRShiftDB/"> *************** *** 12,32 **** <xsd:schema targetNamespace="http://www.nmrshiftdb.org/ws/NMRShiftDB/" ! xmlns:cml="http://www.xml-cml.org/schema/cml2/core"> ! <xsd:import namespace="http://schemas.xmlsoap.org/soap/encoding/"/> ! <xsd:import namespace="http://schemas.xmlsoap.org/wsdl/"/> <xsd:import ! namespace="http://www.xml-cml.org/schema/cml2/core" ! schemaLocation="http://cml.sourceforge.net/schema/cmlCore.xsd"> ! </xsd:import> <xsd:element name="doPredictionResponse" ! type="cml:spectrum" /> <xsd:element name="doPredictionRequest" type="tns:DoPredictionParameters" /> <xsd:complexType name="DoPredictionParameters"> <xsd:sequence> ! <xsd:element ref="cml:molecule" minOccurs="1" maxOccurs="1" /> ! <xsd:element name="spectrumTypeName" type="xsd:string" /> </xsd:sequence> </xsd:complexType> --- 12,38 ---- <xsd:schema targetNamespace="http://www.nmrshiftdb.org/ws/NMRShiftDB/" ! xmlns:cml="http://www.xml-cml.org/schema"> ! <xsd:import namespace="http://schemas.xmlsoap.org/soap/encoding/" /> ! <xsd:import namespace="http://schemas.xmlsoap.org/wsdl/" /> ! <xsd:import namespace="http://www.w3.org/2001/XMLSchema" /> <xsd:import ! namespace="http://www.xml-cml.org/schema" ! schemaLocation="http://almost.cubic.uni-koeln.de/schema.xsd" /> <xsd:element name="doPredictionResponse" ! type="cml:spectrumTypeType" /> <xsd:element name="doPredictionRequest" type="tns:DoPredictionParameters" /> + <xsd:complexType name="DoPredictionParameters"> <xsd:sequence> ! <xsd:element ! ref="cml:molecule" ! minOccurs="1" ! maxOccurs="1" /> ! <xsd:element ! name="spectrumTypeName" ! type="xsd:string" /> </xsd:sequence> </xsd:complexType> *************** *** 66,72 **** </wsdl:binding> <wsdl:service name="NMRShiftDB"> ! <wsdl:port binding="tns:NMRShiftDBSOAP" name="NMRShiftDBSOAP"> ! Â Â Â Â <soap:address location="http://almost.cubic.uni-koeln.de/axis/services/NMRShiftDB"/> ! Â Â Â Â </wsdl:port> </wsdl:service> ! </wsdl:definitions> --- 72,80 ---- </wsdl:binding> <wsdl:service name="NMRShiftDB"> ! <wsdl:port ! binding="tns:NMRShiftDBSOAP" ! name="NMRShiftDBSOAP"> ! <soap:address location="http://almost.cubic.uni-koeln.de/axis/services/NMRShiftDB" /> ! </wsdl:port> </wsdl:service> ! </wsdl:definitions> \ No newline at end of file |
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/html In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv16050/src/html Modified Files: jchempaint-applet-Jama.jar jchempaint-applet-com_ozten.jar jchempaint-applet-core.jar jchempaint-applet-editor-opts.jar jchempaint-applet-editor.jar jchempaint-applet-jas.jar jchempaint-applet-javax_media.jar jchempaint-applet-javax_vecmath.jar jchempaint-applet-nu.jar jchempaint-applet-org.jar jchempaint-applet-org_3pq.jar jchempaint-applet-org_apache.jar jchempaint-applet-org_omegahat.jar jchempaint-applet-org_openscience.jar jchempaint-applet-org_openscience_cdk.jar jchempaint-applet-org_openscience_cdk_applications.jar jchempaint-applet-org_openscience_cdk_applications_jchempaint.jar jchempaint-applet-org_openscience_cdk_config.jar jchempaint-applet-org_openscience_cdk_dict.jar jchempaint-applet-org_openscience_cdk_io.jar jchempaint-applet-org_openscience_cdk_iupac.jar jchempaint-applet-org_openscience_cdk_math.jar 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RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_apache.jar,v retrieving revision 1.16 retrieving revision 1.17 diff -C2 -r1.16 -r1.17 Binary files /tmp/cvszNA0L2 and /tmp/cvs8Z2Jt9 differ Index: jchempaint-applet-org_omegahat.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_omegahat.jar,v retrieving revision 1.16 retrieving revision 1.17 diff -C2 -r1.16 -r1.17 Binary files /tmp/cvsFcZBUa and /tmp/cvsl6K5Ih differ Index: jchempaint-applet-org_openscience.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience.jar,v retrieving revision 1.42 retrieving revision 1.43 diff -C2 -r1.42 -r1.43 Binary files /tmp/cvsQeIRSb and /tmp/cvsVO2nKi differ Index: jchempaint-applet-org_openscience_cdk.jar =================================================================== RCS file: 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From: Stefan K. <sh...@us...> - 2006-06-13 08:53:10
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/doc In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv24546/doc Modified Files: nmrshiftdbhelp.pdf nmrshiftdbhelp.xml Log Message: new images; help Index: nmrshiftdbhelp.pdf =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/doc/nmrshiftdbhelp.pdf,v retrieving revision 1.61 retrieving revision 1.62 diff -C2 -r1.61 -r1.62 Binary files /tmp/cvs3bxxIJ and /tmp/cvsG07lKw differ Index: nmrshiftdbhelp.xml =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/doc/nmrshiftdbhelp.xml,v retrieving revision 1.75 retrieving revision 1.76 diff -C2 -r1.75 -r1.76 *** nmrshiftdbhelp.xml 3 May 2006 09:54:02 -0000 1.75 --- nmrshiftdbhelp.xml 13 Jun 2006 08:53:00 -0000 1.76 *************** *** 168,172 **** <sect3 id="browse"><title>Browsing the Results</title> <para>The results of each search, i.e., the matching records retrieved from the database, are displayed in the "Results" pane in the form of molecular structures. Up to ten records can be shown per page and up to ten pages are accessible via the numerals at the top of the pane. If necessary, further blocks of ten pages can be accessed by clicking on the appropriate Arrow symbol next to the page numbers.</para> ! <para>To view the details of a particular record, first click on the structure of interest in the Results pane (a blue frame highlights the molecule) and then click on the Show Details button. In the right half of the Results pane the structure is shown together with a schematic stick spectrum and a table of atom numbers and assigned chemical shifts. The first structure on a page is shown directly. Instead of choosing a structure you can also browse in a page with the "Browse forward"/"Browse backward" buttons. This can also be used with browsers like Konqueror having difficulties with JavaScript, where direct selections is not possible.</para> <para>Note: the atom numbers (labels) may appear to be rather arbitrary; they are defined by the numbering scheme generated by the structure editor (depends on the order of drawing operations) or present in the mol file used as input. The numbering will most likely not correspond to IUPAC or any other systematic scheme. This is a major inconvenience when comparing data for a variety of related structures.</para> <para>The correlation between atom position in the structure and chemical shift value can be viewed by hovering with the mouse over a shift value in the data table. The corresponding atom in the structure and the peak in the stick spectrum will be highlighted. Pointing with the mouse to a peak in the spectrum causes the shift value to be displayed. You can zoom or expand a desired spectrum region using the mouse to position two lines marking the left and right limits of the expansion. Click "Zoom to original size" to return to the full display.</para> --- 168,172 ---- <sect3 id="browse"><title>Browsing the Results</title> <para>The results of each search, i.e., the matching records retrieved from the database, are displayed in the "Results" pane in the form of molecular structures. Up to ten records can be shown per page and up to ten pages are accessible via the numerals at the top of the pane. If necessary, further blocks of ten pages can be accessed by clicking on the appropriate Arrow symbol next to the page numbers.</para> ! <para>To view the details of a particular record, click on the structure of interest in the Results pane (a light blue frame highlights the molecule). In the right half of the Results pane the structure is shown together with a schematic stick spectrum and a table of atom numbers and assigned chemical shifts. In a lighter color other spectra of the same type are given for compararision. The first structure on a page is shown directly. Instead of choosing a structure you can also browse in a page with the "Browse forward"/"Browse backward" buttons. This can also be used with browsers like Konqueror having difficulties with JavaScript, where direct selections is not possible. In the right half there are two tabs: Spectral Data and Additional Data. The Spectral Data are the spectra you see by default, whereas Additional Data gives text information about Structures (names, weight etc.) and spectrum (measurement conditions etc.). If there are several spectra of one type, they can be viewed by vertical scrolling. Orer is by spectrum type.</para> <para>Note: the atom numbers (labels) may appear to be rather arbitrary; they are defined by the numbering scheme generated by the structure editor (depends on the order of drawing operations) or present in the mol file used as input. The numbering will most likely not correspond to IUPAC or any other systematic scheme. This is a major inconvenience when comparing data for a variety of related structures.</para> <para>The correlation between atom position in the structure and chemical shift value can be viewed by hovering with the mouse over a shift value in the data table. The corresponding atom in the structure and the peak in the stick spectrum will be highlighted. Pointing with the mouse to a peak in the spectrum causes the shift value to be displayed. You can zoom or expand a desired spectrum region using the mouse to position two lines marking the left and right limits of the expansion. Click "Zoom to original size" to return to the full display.</para> |
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From: Stefan K. <sh...@us...> - 2006-06-13 08:53:08
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/html In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv24546/src/html Modified Files: using.html Log Message: new images; help Index: using.html =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/using.html,v retrieving revision 1.43 retrieving revision 1.44 diff -C2 -r1.43 -r1.44 *** using.html 24 Mar 2006 17:43:51 -0000 1.43 --- using.html 13 Jun 2006 08:53:00 -0000 1.44 *************** *** 273,277 **** TARGET="_top" >valid formats</A ! >)) via the "Browse" button or activate the Java based version via the <SPAN CLASS="inlinemediaobject" ><IMG --- 273,277 ---- TARGET="_top" >valid formats</A ! >) via the "Browse" button or activate the Java based version via the <SPAN CLASS="inlinemediaobject" ><IMG *************** *** 428,432 **** >The results of each search, i.e., the matching records retrieved from the database, are displayed in the "Results" pane in the form of molecular structures. Up to ten records can be shown per page and up to ten pages are accessible via the numerals at the top of the pane. If necessary, further blocks of ten pages can be accessed by clicking on the appropriate Arrow symbol next to the page numbers.</P ><P ! >To view the details of a particular record, first click on the structure of interest in the Results pane (a blue frame highlights the molecule) and then click on the Show Details button. In the right half of the Results pane the structure is shown together with a schematic stick spectrum and a table of atom numbers and assigned chemical shifts. The first structure on a page is shown directly. Instead of choosing a structure you can also browse in a page with the "Browse forward"/"Browse backward" buttons. This can also be used with browsers like Konqueror having difficulties with JavaScript, where direct selections is not possible.</P ><P >Note: the atom numbers (labels) may appear to be rather arbitrary; they are defined by the numbering scheme generated by the structure editor (depends on the order of drawing operations) or present in the mol file used as input. The numbering will most likely not correspond to IUPAC or any other systematic scheme. This is a major inconvenience when comparing data for a variety of related structures.</P --- 428,432 ---- >The results of each search, i.e., the matching records retrieved from the database, are displayed in the "Results" pane in the form of molecular structures. Up to ten records can be shown per page and up to ten pages are accessible via the numerals at the top of the pane. If necessary, further blocks of ten pages can be accessed by clicking on the appropriate Arrow symbol next to the page numbers.</P ><P ! >To view the details of a particular record, click on the structure of interest in the Results pane (a light blue frame highlights the molecule). In the right half of the Results pane the structure is shown together with a schematic stick spectrum and a table of atom numbers and assigned chemical shifts. In a lighter color other spectra of the same type are given for compararision. The first structure on a page is shown directly. Instead of choosing a structure you can also browse in a page with the "Browse forward"/"Browse backward" buttons. This can also be used with browsers like Konqueror having difficulties with JavaScript, where direct selections is not possible. In the right half there are two tabs: Spectral Data and Additional Data. The Spectral Data are the spectra you see by default, whereas Additional Data gives text information about Structures (names, weight etc.) and spectrum (measurement conditions etc.). If there are several spectra of one type, they can be viewed by vertical scrolling. Orer is by spectrum type.</P ><P >Note: the atom numbers (labels) may appear to be rather arbitrary; they are defined by the numbering scheme generated by the structure editor (depends on the order of drawing operations) or present in the mol file used as input. The numbering will most likely not correspond to IUPAC or any other systematic scheme. This is a major inconvenience when comparing data for a variety of related structures.</P *************** *** 436,444 **** >The molecular structure and/or spectrum can be viewed or downloaded in various formats. Choose a format and click the "Request" button. If you are a registered contributor, you can also add a new spectrum for an existing molecule in the database by clicking the "Add a spectrum" button. A database record of particular interest can be added to a "favorites" list by clicking the "Bookmark" button. The name of the structure will then be displayed in the bookmarks section at the top of the page and you can recall the structure by clicking it's bookmard name.</P ><P ! >The structure shown in the Details window can be manipulated (scaling, translation, rotation) via a menu which can be accessed by pressing the right mouse button while in the structure window. For more information, see the link to <A ! HREF="chemaxon/marvin/help/view.html" ! TARGET="_top" ! >Marvin Help</A ! >.</P ></DIV ><DIV --- 436,442 ---- >The molecular structure and/or spectrum can be viewed or downloaded in various formats. Choose a format and click the "Request" button. If you are a registered contributor, you can also add a new spectrum for an existing molecule in the database by clicking the "Add a spectrum" button. A database record of particular interest can be added to a "favorites" list by clicking the "Bookmark" button. The name of the structure will then be displayed in the bookmarks section at the top of the page and you can recall the structure by clicking it's bookmard name.</P ><P ! >The structure shown in the Details window is shown as a graphic or, if you are in Java mode, via the JChemPaint or JMol applet, depending on if you have got 2d- or 3d-coordinates. The structure in JMol can be manipulated (scaling, translation, rotation) via a menu which can be accessed by pressing the right mouse button while in the structure window.</P ! ><P ! >The link described as "Copy molecule link" on the bottom of the page can be used as an external link to exactly this dataset without searching for it. For copying it, use the context menu (right click with the mouse) of your browser.</P ></DIV ><DIV *************** *** 466,470 **** HREF="using.html#register" >registered user</A ! >. Please do not use the "back" and "forward" button of your browser while doing a submit. To do a submit, click on the "Submit molecule" tab. In the first step, you may enter literature references for your data. If custom identifiers (e. g. letters) for atoms are used in the literature you want to enter, mark this literature in the first colum. Then press "Submit literatures". You then need to enter the strucure for your spectrum. You can either upload a file in common formats (MDL Molfiles, RGfiles, SDfiles, REACCS Rxnfiles, RDfiles, compressed molfile, SMILES, SMARTS, PDB or XYZ) via the "Choose file..." button or activate the Java based version. You can then use the JChemPaint applet to interactivly paint structues. You can also import a file by Copy & Paste via the "Import text by copy &paste button". You do not need to (but you may) draw implicit hydrogens. After you drew or imported your structure, submit it by clicking the submit button. Your structures are collected in the <A HREF="using.html#struchistory" >structures history</A --- 464,476 ---- HREF="using.html#register" >registered user</A ! >. Please do not use the "back" and "forward" button of your browser while doing a submit. To do a submit, click on the "Submit molecule" tab. In the first step, you may enter literature references for your data. If custom identifiers (e. g. letters) for atoms are used in the literature you want to enter, mark this literature in the first colum. Then press "Submit literatures". You then need to enter the strucure for your spectrum. You can either upload a file in common formats (<A ! HREF="nmrshiftdbhtml/formats.jsp" ! TARGET="_top" ! >valid formats</A ! >) via the "Choose file..." button or activate the Java based version via the <SPAN ! CLASS="inlinemediaobject" ! ><IMG ! SRC="../images/mug.gif"></SPAN ! > symbol. You can then use the JChemPaint applet to interactivly paint structues. You can also import a file by Copy & Paste via the "Import text by copy &paste button". You do not need to (but you may) draw implicit hydrogens. After you drew or imported your structure, submit it by clicking the submit button. Your structures are collected in the <A HREF="using.html#struchistory" >structures history</A |
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From: Stefan K. <sh...@us...> - 2006-06-13 08:53:06
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/images In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv24546/src/conf/jetspeed/images Added Files: 3D.png java.png Removed Files: 3d.gif mug.gif Log Message: new images; help --- NEW FILE: 3D.png --- PNG (:Æ4Õý LB$H*®º"êZè*º é¢.Â?¼tQ ýHKÂBi63Ýt+7mgg;?ßé=»Ýù Î÷óï{¾ç}Îó;l½Ó4-x7'U2M»ÄÖAcc *ÓVhì§qèl}>wØ`Ø ðú«ØB{¼N£Û ©PU5ç8MgR±®Öã%þm % ¦%ÈL¥^}^Áï±,ÍÕ.$> ~£Ðf Jí ÃB$#3¼~Ö3ÐB¯¤ÐÓ×±D óálùdd¬@!PÒ!È1 ŲD7ó¤²Aã k{½¹N» II·ÔÞY --- NEW FILE: java.png --- PNG %,N á cyrä6K±ëÙá± hDjÚ´BÿL n!8MÆ-éê¨âÏG¾_õ"à| 3Ò¡ Ã2£G!bY*¤Ø*kÃÑ2âÃð"¦ lòâ --- 3d.gif DELETED --- --- mug.gif DELETED --- |
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From: Stefan K. <sh...@us...> - 2006-06-13 08:53:06
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv24546/src/java/org/openscience/nmrshiftdb/om Modified Files: DBSpectrum.java Log Message: new images; help Index: DBSpectrum.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/DBSpectrum.java,v retrieving revision 1.174 retrieving revision 1.175 diff -C2 -r1.174 -r1.175 *** DBSpectrum.java 12 Jun 2006 16:23:56 -0000 1.174 --- DBSpectrum.java 13 Jun 2006 08:53:00 -0000 1.175 *************** *** 80,83 **** --- 80,84 ---- Vector literaturesNew=null; Vector keywordsVector=null; + int otherspectrastringsize=-1; *************** *** 1398,1402 **** Vector spectra=this.getDBMolecule().getDBSpectrums(crit); for(int i=0;i<spectra.size();i++){ ! sb.append("<th bgcolor=\"#0000F8\">"+((DBSpectrum)spectra.get(i)).getKeywords()+"</th>"); } return sb.toString(); --- 1399,1403 ---- Vector spectra=this.getDBMolecule().getDBSpectrums(crit); for(int i=0;i<spectra.size();i++){ ! sb.append("<th bgcolor=\"#0000F8\"><div style=\"color:white\">"+((DBSpectrum)spectra.get(i)).getKeywords()+"</div></th>"); } return sb.toString(); *************** *** 1469,1472 **** --- 1470,1475 ---- public int getOtherSpectraStringSize() throws Exception{ + if(otherspectrastringsize>-1) + return otherspectrastringsize; Criteria crit=new Criteria(); crit.add(DBSpectrumPeer.REVIEW_FLAG,"true"); |
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From: Stefan K. <sh...@us...> - 2006-06-13 08:53:06
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv24546/src/vmtemplates Modified Files: details.vm predict.vm searchByStructure.vm submit.vm Log Message: new images; help Index: details.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/details.vm,v retrieving revision 1.153 retrieving revision 1.154 diff -C2 -r1.153 -r1.154 *** details.vm 12 Jun 2006 16:23:56 -0000 1.153 --- details.vm 13 Jun 2006 08:53:00 -0000 1.154 *************** *** 131,137 **** #else #if($mol.hasAny3d()) ! <a href="$data.getRequest().getRequestURI();jsessionid=$data.getSession().getId()?$data.getRequest().getQueryString()&applet=applet" title="We have 3d coordinates for this molecule" style="color:white"><img src="images/3d.gif"></a> #end ! <a href="$data.getRequest().getRequestURI();jsessionid=$data.getSession().getId()?$data.getRequest().getQueryString()&applet=applet" title="Switch on Java-Applets" style="color:white"><img src="images/mug.gif"></a><br> <img src="$image"> #end --- 131,137 ---- #else #if($mol.hasAny3d()) ! <a href="$data.getRequest().getRequestURI();jsessionid=$data.getSession().getId()?$data.getRequest().getQueryString()&applet=applet" title="We have 3d coordinates for this molecule" style="color:white"><img src="images/3D.png"></a> #end ! <a href="$data.getRequest().getRequestURI();jsessionid=$data.getSession().getId()?$data.getRequest().getQueryString()&applet=applet" title="Switch on Java-Applets" style="color:white"><img src="images/java.png"></a><br> <img src="$image"> #end Index: predict.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/predict.vm,v retrieving revision 1.79 retrieving revision 1.80 diff -C2 -r1.79 -r1.80 *** predict.vm 31 May 2006 15:01:01 -0000 1.79 --- predict.vm 13 Jun 2006 08:53:00 -0000 1.80 *************** *** 65,69 **** <img src="$imagefile"> #end ! <a href="$request.getRequestURI();jsessionid=$session.getId()?$request.getQueryString()&applet=applet" title="Switch on Java-Applets" style="color:white"><img src="images/mug.gif"></a> #end <form action="portal/pane0/Predict;jsessionid=$session.getId()" enctype="multipart/form-data" name="uploadform" method="post"> --- 65,69 ---- <img src="$imagefile"> #end ! <a href="$request.getRequestURI();jsessionid=$session.getId()?$request.getQueryString()&applet=applet" title="Switch on Java-Applets" style="color:white"><img src="images/java.png"></a> #end <form action="portal/pane0/Predict;jsessionid=$session.getId()" enctype="multipart/form-data" name="uploadform" method="post"> Index: searchByStructure.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/searchByStructure.vm,v retrieving revision 1.61 retrieving revision 1.62 diff -C2 -r1.61 -r1.62 *** searchByStructure.vm 17 May 2006 13:20:34 -0000 1.61 --- searchByStructure.vm 13 Jun 2006 08:53:00 -0000 1.62 *************** *** 40,44 **** <img src="$imagefile"> #end ! <a href="$data.getRequest().getRequestURI();jsessionid=$data.getSession().getId()?$data.getRequest().getQueryString()&applet=applet" title="Switch on Java-Applets" style="color:white"><img src="images/mug.gif"></a><br><br> #end </td> --- 40,44 ---- <img src="$imagefile"> #end ! <a href="$data.getRequest().getRequestURI();jsessionid=$data.getSession().getId()?$data.getRequest().getQueryString()&applet=applet" title="Switch on Java-Applets" style="color:white"><img src="images/java.png"></a><br><br> #end </td> Index: submit.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/submit.vm,v retrieving revision 1.153 retrieving revision 1.154 diff -C2 -r1.153 -r1.154 *** submit.vm 17 May 2006 13:20:34 -0000 1.153 --- submit.vm 13 Jun 2006 08:53:00 -0000 1.154 *************** *** 331,335 **** #end <br> ! <a href="$request.getRequestURI();jsessionid=$session.getId()?applet=applet" title="Switch on Java-Applets" style="color:white"><img src="images/mug.gif"></a> #end #if($subdata.getLevel()==1) --- 331,335 ---- #end <br> ! <a href="$request.getRequestURI();jsessionid=$session.getId()?applet=applet" title="Switch on Java-Applets" style="color:white"><img src="images/java.png"></a> #end #if($subdata.getLevel()==1) |
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From: Stefan K. <sh...@us...> - 2006-06-12 16:24:10
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv13017/src/java/org/openscience/nmrshiftdb/om Modified Files: DBSpectrum.java Log Message: better layout Index: DBSpectrum.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/DBSpectrum.java,v retrieving revision 1.173 retrieving revision 1.174 diff -C2 -r1.173 -r1.174 *** DBSpectrum.java 9 Jun 2006 19:42:56 -0000 1.173 --- DBSpectrum.java 12 Jun 2006 16:23:56 -0000 1.174 *************** *** 1388,1391 **** --- 1388,1407 ---- + public String getOtherSpectraStringHeader() throws Exception{ + StringBuffer sb=new StringBuffer(); + Criteria crit=new Criteria(); + crit.addOrderByColumn(DBSpectrumPeer.SPECTRUM_ID); + crit.add(DBSpectrumPeer.REVIEW_FLAG,"true"); + crit.add(DBSpectrumPeer.SPECTRUM_TYPE_ID, this.getSpectrumTypeId()); + crit.add(DBSpectrumPeer.SPECTRUM_ID,this.getSpectrumId(),Criteria.NOT_EQUAL); + crit.add(DBSpectrumPeer.MOLECULE_ID,this.getMoleculeId()); + Vector spectra=this.getDBMolecule().getDBSpectrums(crit); + for(int i=0;i<spectra.size();i++){ + sb.append("<th bgcolor=\"#0000F8\">"+((DBSpectrum)spectra.get(i)).getKeywords()+"</th>"); + } + return sb.toString(); + } + + public String getOtherSpectraString(int atomNumber) throws Exception{ DBAtom assignedTo=this.getDBMolecule().getAtomAt(atomNumber); *************** *** 1394,1454 **** crit.addOrderByColumn(DBSpectrumPeer.SPECTRUM_ID); crit.add(DBSpectrumPeer.REVIEW_FLAG,"true"); Vector spectra=this.getDBMolecule().getDBSpectrums(crit); for(int i=0;i<spectra.size();i++){ DBSpectrum spectrum=(DBSpectrum)spectra.get(i); ! if(!spectrum.getSpectrumId().equals(this.getSpectrumId()) && spectrum.getSpectrumTypeId().equals(this.getSpectrumTypeId())){ ! if(this.getDBSpectrumType().getDBIsotope(1).getElementSymbol().equals("H")){ ! Vector connatoms=assignedTo.getConnectedAtoms(); ! int connhs=0; for(int k=0;k<connatoms.size();k++){ if(((DBAtom)connatoms.get(k)).getSymbol().equals("H")){ ! connhs++; ! } ! } ! if(connhs==2){ ! for(int k=0;k<connatoms.size();k++){ ! if(((DBAtom)connatoms.get(k)).getSymbol().equals("H")){ ! Criteria crit2=new Criteria(); ! crit2.addJoin(DBSignalDBAtomPeer.SIGNAL_ID,DBSignalPeer.SIGNAL_ID); ! crit2.add(DBSignalDBAtomPeer.ATOM_ID,((DBAtom)connatoms.get(k)).getAtomId()); ! crit2.add(DBSignalPeer.SPECTRUM_ID,spectrum.getSpectrumId()); ! Vector v=DBSignalPeer.doSelect(crit2); ! if(v.size()>0){ ! DBSignal signal=(DBSignal)v.get(0); ! sb.append("<td>"+signal.getFirstShift().getValue()+"</td>"); ! break; ! } } } ! }else{ ! for(int k=0;k<connatoms.size();k++){ ! if(((DBAtom)connatoms.get(k)).getSymbol().equals("H")){ ! Criteria crit2=new Criteria(); ! crit2.addJoin(DBSignalDBAtomPeer.SIGNAL_ID,DBSignalPeer.SIGNAL_ID); ! crit2.add(DBSignalDBAtomPeer.ATOM_ID,((DBAtom)connatoms.get(k)).getAtomId()); ! crit2.add(DBSignalPeer.SPECTRUM_ID,spectrum.getSpectrumId()); ! Vector v=DBSignalPeer.doSelect(crit2); ! if(v.size()>0){ ! DBSignal signal=(DBSignal)v.get(0); ! sb.append("<td>"+signal.getFirstShift().getValue()+"</td>"); ! break; ! } } } } - }else{ - Criteria crit2=new Criteria(); - crit2.addJoin(DBSignalDBAtomPeer.SIGNAL_ID,DBSignalPeer.SIGNAL_ID); - crit2.add(DBSignalDBAtomPeer.ATOM_ID,assignedTo.getAtomId()); - crit2.add(DBSignalPeer.SPECTRUM_ID,spectrum.getSpectrumId()); - DBSignal signal=(DBSignal)DBSignalPeer.doSelect(crit2).get(0); - sb.append("<td>"+signal.getFirstShift().getValue()+"</td>"); } } } return sb.toString(); } public int getOtherSpectraStringSize() throws Exception{ - StringBuffer sb=new StringBuffer(); Criteria crit=new Criteria(); crit.add(DBSpectrumPeer.REVIEW_FLAG,"true"); --- 1410,1472 ---- crit.addOrderByColumn(DBSpectrumPeer.SPECTRUM_ID); crit.add(DBSpectrumPeer.REVIEW_FLAG,"true"); + crit.add(DBSpectrumPeer.SPECTRUM_TYPE_ID, this.getSpectrumTypeId()); + crit.add(DBSpectrumPeer.SPECTRUM_ID,this.getSpectrumId(),Criteria.NOT_EQUAL); + crit.add(DBSpectrumPeer.MOLECULE_ID,this.getMoleculeId()); Vector spectra=this.getDBMolecule().getDBSpectrums(crit); for(int i=0;i<spectra.size();i++){ DBSpectrum spectrum=(DBSpectrum)spectra.get(i); ! if(this.getDBSpectrumType().getDBIsotope(1).getElementSymbol().equals("H")){ ! Vector connatoms=assignedTo.getConnectedAtoms(); ! int connhs=0; ! for(int k=0;k<connatoms.size();k++){ ! if(((DBAtom)connatoms.get(k)).getSymbol().equals("H")){ ! connhs++; ! } ! } ! if(connhs==2){ for(int k=0;k<connatoms.size();k++){ if(((DBAtom)connatoms.get(k)).getSymbol().equals("H")){ ! Criteria crit2=new Criteria(); ! crit2.addJoin(DBSignalDBAtomPeer.SIGNAL_ID,DBSignalPeer.SIGNAL_ID); ! crit2.add(DBSignalDBAtomPeer.ATOM_ID,((DBAtom)connatoms.get(k)).getAtomId()); ! crit2.add(DBSignalPeer.SPECTRUM_ID,spectrum.getSpectrumId()); ! Vector v=DBSignalPeer.doSelect(crit2); ! if(v.size()>0){ ! DBSignal signal=(DBSignal)v.get(0); ! sb.append("<td bgcolor=\"#E8E8E8\">"+signal.getFirstShift().getValue()+"</td>"); ! break; } } ! } ! }else{ ! for(int k=0;k<connatoms.size();k++){ ! if(((DBAtom)connatoms.get(k)).getSymbol().equals("H")){ ! Criteria crit2=new Criteria(); ! crit2.addJoin(DBSignalDBAtomPeer.SIGNAL_ID,DBSignalPeer.SIGNAL_ID); ! crit2.add(DBSignalDBAtomPeer.ATOM_ID,((DBAtom)connatoms.get(k)).getAtomId()); ! crit2.add(DBSignalPeer.SPECTRUM_ID,spectrum.getSpectrumId()); ! Vector v=DBSignalPeer.doSelect(crit2); ! if(v.size()>0){ ! DBSignal signal=(DBSignal)v.get(0); ! sb.append("<td bgcolor=\"#E8E8E8\">"+signal.getFirstShift().getValue()+"</td>"); ! break; } } } } + }else{ + Criteria crit2=new Criteria(); + crit2.addJoin(DBSignalDBAtomPeer.SIGNAL_ID,DBSignalPeer.SIGNAL_ID); + crit2.add(DBSignalDBAtomPeer.ATOM_ID,assignedTo.getAtomId()); + crit2.add(DBSignalPeer.SPECTRUM_ID,spectrum.getSpectrumId()); + DBSignal signal=(DBSignal)DBSignalPeer.doSelect(crit2).get(0); + sb.append("<td bgcolor=\"#E8E8E8\">"+signal.getFirstShift().getValue()+"</td>"); } } return sb.toString(); } + + public int getOtherSpectraStringSize() throws Exception{ Criteria crit=new Criteria(); crit.add(DBSpectrumPeer.REVIEW_FLAG,"true"); *************** *** 1457,1478 **** crit.add(DBSpectrumPeer.SPECTRUM_ID,this.getSpectrumId(),Criteria.NOT_EQUAL); Vector spectra=this.getDBMolecule().getDBSpectrums(crit); - System.err.println(spectra.size()); - System.err.println(spectra.size()); - System.err.println(spectra.size()); - System.err.println(spectra.size()); - System.err.println(spectra.size()); - System.err.println(spectra.size()); - System.err.println(spectra.size()); - System.err.println(spectra.size()); - System.err.println(spectra.size()); - System.err.println(spectra.size()); - System.err.println(spectra.size()); - System.err.println(spectra.size()); - System.err.println(spectra.size()); - System.err.println(spectra.size()); - System.err.println(spectra.size()); - System.err.println(spectra.size()); - System.err.println(spectra.size()); - System.err.println(spectra.size()); return(spectra.size()); } --- 1475,1478 ---- |
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From: Stefan K. <sh...@us...> - 2006-06-12 16:23:59
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv13017/src/vmtemplates Modified Files: details.vm Log Message: better layout Index: details.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/details.vm,v retrieving revision 1.152 retrieving revision 1.153 diff -C2 -r1.152 -r1.153 *** details.vm 9 Jun 2006 19:42:56 -0000 1.152 --- details.vm 12 Jun 2006 16:23:56 -0000 1.153 *************** *** 177,181 **** #end #if($spectrum.getOtherSpectraStringSize()>0) ! <th rowspan="$spectrum.getOtherSpectraStringSize()"><div style="color:white">Other spectra for that structure and spectrum type</div></th> #end </tr> --- 177,181 ---- #end #if($spectrum.getOtherSpectraStringSize()>0) ! <th bgcolor="#FFFFFF" width="10"></th>$spectrum.getOtherSpectraStringHeader() #end </tr> *************** *** 211,215 **** <td>$option.getIntensity()</td> #end ! $spectrum.getOtherSpectraString($option.getValue().intValue()) </tr> #end --- 211,217 ---- <td>$option.getIntensity()</td> #end ! #if($spectrum.getOtherSpectraStringSize()>0) ! <td width="10" bgcolor="#FFFFFF"></td>$spectrum.getOtherSpectraString($option.getValue().intValue()) ! #end </tr> #end |
Update of /cvsroot/nmrshiftdb/nmrshiftdb/lib In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv23464/lib Modified Files: cdk-builder3d.jar cdk-charges.jar cdk-core.jar cdk-data.jar cdk-extra.jar cdk-forcefield.jar cdk-interfaces.jar cdk-io.jar cdk-libio-cml.jar cdk-pdb-cml.jar cdk-pdb.jar cdk-qsar-cml.jar cdk-qsar.jar cdk-render.jar cdk-smiles.jar cdk-standard.jar cdk-valencycheck.jar Log Message: new cdk Index: cdk-builder3d.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-builder3d.jar,v retrieving revision 1.47 retrieving revision 1.48 diff -C2 -r1.47 -r1.48 Binary files /tmp/cvsntiG2R and /tmp/cvsvH7Seu differ Index: cdk-charges.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-charges.jar,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -r1.2 -r1.3 Binary files /tmp/cvsP6BFuS and /tmp/cvs8WtwNu differ Index: cdk-core.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-core.jar,v retrieving revision 1.119 retrieving revision 1.120 diff -C2 -r1.119 -r1.120 Binary files /tmp/cvsN0frbS and /tmp/cvsVRADxu differ Index: cdk-data.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-data.jar,v retrieving revision 1.43 retrieving revision 1.44 diff -C2 -r1.43 -r1.44 Binary files /tmp/cvsvMrrFV and /tmp/cvsoiRK3x differ Index: cdk-extra.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-extra.jar,v retrieving revision 1.157 retrieving revision 1.158 diff -C2 -r1.157 -r1.158 Binary files /tmp/cvsWs2daX and /tmp/cvszNDiDz differ Index: cdk-forcefield.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-forcefield.jar,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -r1.2 -r1.3 Binary files /tmp/cvsWqmBd0 and /tmp/cvs36pYJC differ Index: cdk-interfaces.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-interfaces.jar,v retrieving revision 1.35 retrieving revision 1.36 diff -C2 -r1.35 -r1.36 Binary files /tmp/cvsBLBG11 and /tmp/cvsgtYcAE differ Index: cdk-io.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-io.jar,v retrieving revision 1.109 retrieving revision 1.110 diff -C2 -r1.109 -r1.110 Binary files /tmp/cvs5ZqC42 and /tmp/cvsFrccHF differ Index: cdk-libio-cml.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-libio-cml.jar,v retrieving revision 1.35 retrieving revision 1.36 diff -C2 -r1.35 -r1.36 Binary files /tmp/cvsQxR923 and /tmp/cvsyS38IG differ Index: cdk-pdb-cml.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-pdb-cml.jar,v retrieving revision 1.35 retrieving revision 1.36 diff -C2 -r1.35 -r1.36 Binary files /tmp/cvsUnw0E7 and /tmp/cvsDf8JmK differ Index: cdk-pdb.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-pdb.jar,v retrieving revision 1.35 retrieving revision 1.36 diff -C2 -r1.35 -r1.36 Binary files /tmp/cvsXqlql6 and /tmp/cvsyMn14I differ Index: cdk-qsar-cml.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-qsar-cml.jar,v retrieving revision 1.35 retrieving revision 1.36 diff -C2 -r1.35 -r1.36 Binary files /tmp/cvspUwxH9 and /tmp/cvsdBHUsM differ Index: cdk-qsar.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-qsar.jar,v retrieving revision 1.50 retrieving revision 1.51 diff -C2 -r1.50 -r1.51 Binary files /tmp/cvs7O6aA8 and /tmp/cvsI1mroL differ Index: cdk-render.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-render.jar,v retrieving revision 1.90 retrieving revision 1.91 diff -C2 -r1.90 -r1.91 Binary files /tmp/cvslvhvAa and /tmp/cvs5V9arN differ Index: cdk-smiles.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-smiles.jar,v retrieving revision 1.5 retrieving revision 1.6 diff -C2 -r1.5 -r1.6 Binary files /tmp/cvs2vmB7d and /tmp/cvs0PMd0Q differ Index: cdk-standard.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-standard.jar,v retrieving revision 1.104 retrieving revision 1.105 diff -C2 -r1.104 -r1.105 Binary files /tmp/cvs0DBkSc and /tmp/cvsYCsHNP differ Index: cdk-valencycheck.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/lib/cdk-valencycheck.jar,v retrieving revision 1.5 retrieving revision 1.6 diff -C2 -r1.5 -r1.6 Binary files /tmp/cvsSfUaUg and /tmp/cvsqc6yRT differ |
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From: Stefan K. <sh...@us...> - 2006-06-12 15:04:20
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv5728/src/java/org/openscience/nmrshiftdb/portlets Modified Files: SubmitPortlet.java Log Message: corrects a problem with review Index: SubmitPortlet.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets/SubmitPortlet.java,v retrieving revision 1.412 retrieving revision 1.413 diff -C2 -r1.412 -r1.413 *** SubmitPortlet.java 8 Jun 2006 11:02:36 -0000 1.412 --- SubmitPortlet.java 12 Jun 2006 15:04:16 -0000 1.413 *************** *** 1555,1567 **** } if (!error) { - try{ ! new ReviewPortlet().review(runData, NmrshiftdbConstants.TRUE, subData.spectrumid); } catch (Exception ex) { return new StringElement(GeneralUtils.logError(ex, "SubmitPortlet/Edit/populate subData", runData,true)); } - - - if (showMessageWithReviewer) { try { --- 1555,1565 ---- } if (!error) { try{ ! if(subData.accept!=null){ ! new ReviewPortlet().review(runData, NmrshiftdbConstants.TRUE, subData.spectrumid); ! } } catch (Exception ex) { return new StringElement(GeneralUtils.logError(ex, "SubmitPortlet/Edit/populate subData", runData,true)); } if (showMessageWithReviewer) { try { |
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From: Stefan K. <sh...@us...> - 2006-06-12 13:57:31
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv8127/src/java/org/openscience/nmrshiftdb/webservices Modified Files: NMRShiftDBServiceBindingImpl.java Log Message: this is the cml-only webservice Index: NMRShiftDBServiceBindingImpl.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices/NMRShiftDBServiceBindingImpl.java,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -r1.2 -r1.3 *** NMRShiftDBServiceBindingImpl.java 12 Jun 2006 11:27:29 -0000 1.2 --- NMRShiftDBServiceBindingImpl.java 12 Jun 2006 13:57:22 -0000 1.3 *************** *** 5,8 **** --- 5,11 ---- import java.util.HashMap; + import javax.xml.parsers.DocumentBuilder; + import javax.xml.parsers.DocumentBuilderFactory; + import nu.xom.Document; import nu.xom.Node; *************** *** 24,28 **** public org.w3c.dom.Document doPrediction(org.w3c.dom.Document request) throws RemoteException { ! org.w3c.dom.Document responsedocument = null; try{ Document doc=DOMConverter.convert(request); --- 27,31 ---- public org.w3c.dom.Document doPrediction(org.w3c.dom.Document request) throws RemoteException { ! org.w3c.dom.Document document = null; try{ Document doc=DOMConverter.convert(request); *************** *** 40,43 **** --- 43,47 ---- dbspectype=DBSpectrumTypePeer.getByName(spectype); CMLSpectrum spectrum=new CMLSpectrum(); + spectrum.setNamespaceURI("http://www.xml-cml.org/schema/cml2/spect"); CMLPeakList peakList=new CMLPeakList(); spectrum.addPeakList(peakList); *************** *** 54,61 **** } } }catch(Exception ex){ throw new RemoteException(ex.getMessage(),ex); } ! return responsedocument; } --- 58,68 ---- } } + DocumentBuilder builder; + builder = DocumentBuilderFactory.newInstance().newDocumentBuilder(); + document = builder.parse(new ByteArrayInputStream(spectrum.toXML().getBytes())); }catch(Exception ex){ throw new RemoteException(ex.getMessage(),ex); } ! return document; } |
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From: Stefan K. <sh...@us...> - 2006-06-12 13:57:24
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/tests In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv8127/src/java/org/openscience/nmrshiftdb/tests Modified Files: NMRShiftDBServicesTest.java Log Message: this is the cml-only webservice Index: NMRShiftDBServicesTest.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/tests/NMRShiftDBServicesTest.java,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -r1.2 -r1.3 *** NMRShiftDBServicesTest.java 8 Jun 2006 11:02:36 -0000 1.2 --- NMRShiftDBServicesTest.java 12 Jun 2006 13:57:22 -0000 1.3 *************** *** 67,71 **** e = elem.getAsDOM(); System.err.println(XMLUtils.ElementToString(e)); ! assertEquals(4,e.getChildNodes().getLength()); } --- 67,71 ---- e = elem.getAsDOM(); System.err.println(XMLUtils.ElementToString(e)); ! assertEquals(1,e.getChildNodes().getLength()); } |
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From: Stefan K. <sh...@us...> - 2006-06-12 11:27:34
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv6014/src/java/org/openscience/nmrshiftdb/webservices Modified Files: NMRShiftDBServiceBindingImpl.java Log Message: changes response type of web service to cml spectrum Index: NMRShiftDBServiceBindingImpl.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices/NMRShiftDBServiceBindingImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -r1.1 -r1.2 *** NMRShiftDBServiceBindingImpl.java 7 Jun 2006 19:13:50 -0000 1.1 --- NMRShiftDBServiceBindingImpl.java 12 Jun 2006 11:27:29 -0000 1.2 *************** *** 5,13 **** import java.util.HashMap; - import javax.xml.parsers.DocumentBuilder; - import javax.xml.parsers.DocumentBuilderFactory; - import nu.xom.Document; - import nu.xom.Element; import nu.xom.Node; import nu.xom.converters.DOMConverter; --- 5,9 ---- *************** *** 21,24 **** --- 17,23 ---- import org.openscience.nmrshiftdb.om.DBSpectrumType; import org.openscience.nmrshiftdb.om.DBSpectrumTypePeer; + import org.xmlcml.cml.element.CMLPeak; + import org.xmlcml.cml.element.CMLPeakList; + import org.xmlcml.cml.element.CMLSpectrum; public class NMRShiftDBServiceBindingImpl implements NMRShiftDB { *************** *** 40,62 **** if(!spectype.equals("All")) dbspectype=DBSpectrumTypePeer.getByName(spectype); ! DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); ! DocumentBuilder builder = factory.newDocumentBuilder(); ! responsedocument = builder.newDocument(); ! org.w3c.dom.Element root =(org.w3c.dom.Element)responsedocument.createElementNS("http://www.nmrshiftdb.org/ws/NMRShiftDB/","PredictionList"); ! responsedocument.appendChild(root); for(int i=0;i<mol.getAtomCount();i++){ - org.w3c.dom.Element predictionlistelement= (org.w3c.dom.Element)responsedocument.createElementNS("http://www.nmrshiftdb.org/ws/NMRShiftDB/","PredictionListElement"); if(spectype.equals("All") || dbspectype.getDBIsotope(1).getElementSymbol().equals(mol.getAtomAt(i).getSymbol())){ double[] result=PredictionTool.generalPredict(mol,mol.getAtomAt(i),false,true,-1,-1,new StringBuffer(),false,false,null,new HashMap(),-1,true,new StringBuffer(),6,true,true); ! org.w3c.dom.Element min=(org.w3c.dom.Element)responsedocument.createElementNS("http://www.nmrshiftdb.org/ws/NMRShiftDB/","min"); ! min.appendChild(responsedocument.createTextNode(result[0]+"")); ! predictionlistelement.appendChild(min); ! org.w3c.dom.Element value=(org.w3c.dom.Element)responsedocument.createElementNS("http://www.nmrshiftdb.org/ws/NMRShiftDB/","value"); ! value.appendChild(responsedocument.createTextNode(""+result[1]) ); ! predictionlistelement.appendChild(value); ! org.w3c.dom.Element max=(org.w3c.dom.Element)responsedocument.createElementNS("http://www.nmrshiftdb.org/ws/NMRShiftDB/","max"); ! max.appendChild(responsedocument.createTextNode(result[2]+"")); ! predictionlistelement.appendChild(max); ! root.appendChild(predictionlistelement); } } --- 39,55 ---- if(!spectype.equals("All")) dbspectype=DBSpectrumTypePeer.getByName(spectype); ! CMLSpectrum spectrum=new CMLSpectrum(); ! CMLPeakList peakList=new CMLPeakList(); ! spectrum.addPeakList(peakList); for(int i=0;i<mol.getAtomCount();i++){ if(spectype.equals("All") || dbspectype.getDBIsotope(1).getElementSymbol().equals(mol.getAtomAt(i).getSymbol())){ double[] result=PredictionTool.generalPredict(mol,mol.getAtomAt(i),false,true,-1,-1,new StringBuffer(),false,false,null,new HashMap(),-1,true,new StringBuffer(),6,true,true); ! CMLPeak peak=new CMLPeak(); ! peak.setXMin(result[0]); ! peak.setXValue(result[1]); ! peak.setXMax(result[1]); ! peak.setXUnits("units:ppm"); ! peak.setId("p"+i); ! peakList.addPeak(peak); } } |
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From: Stefan K. <sh...@us...> - 2006-06-12 11:27:31
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/deploymentdescriptors In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv6014/src/deploymentdescriptors Modified Files: NMRShiftDB.wsdl Log Message: changes response type of web service to cml spectrum Index: NMRShiftDB.wsdl =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/deploymentdescriptors/NMRShiftDB.wsdl,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -r1.3 -r1.4 *** NMRShiftDB.wsdl 8 Jun 2006 16:21:41 -0000 1.3 --- NMRShiftDB.wsdl 12 Jun 2006 11:27:28 -0000 1.4 *************** *** 21,25 **** <xsd:element name="doPredictionResponse" ! type="tns:PredictionList" /> <xsd:element name="doPredictionRequest" --- 21,25 ---- <xsd:element name="doPredictionResponse" ! type="cml:spectrum" /> <xsd:element name="doPredictionRequest" *************** *** 31,53 **** </xsd:sequence> </xsd:complexType> - <xsd:complexType name="PredictionList"> - <xsd:all> - <xsd:element name="PredictionListElements" type="tns:PredictionListElementArray" /> - </xsd:all> - </xsd:complexType> - <xsd:complexType name="PredictionListElementArray"> - <xsd:complexContent> - <xsd:restriction base="soapenc:Array"> - <xsd:attribute ref="soapenc:arrayType" wsdl:arrayType="tns:PredictionListElement[]" /> - </xsd:restriction> - </xsd:complexContent> - </xsd:complexType> - <xsd:complexType name="PredictionListElement"> - <xsd:all> - <xsd:element name="min" type="xsd:double" /> - <xsd:element name="value" type="xsd:double" /> - <xsd:element name="mix" type="xsd:double" /> - </xsd:all> - </xsd:complexType> </xsd:schema> </wsdl:types> --- 31,34 ---- |
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From: Stefan K. <sh...@us...> - 2006-06-12 10:51:25
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/html In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv20763/src/html Modified Files: marvin.js Log Message: agjklöasdg Index: marvin.js =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/marvin.js,v retrieving revision 1.22 retrieving revision 1.23 diff -C2 -r1.22 -r1.23 *** marvin.js 17 Jan 2006 10:13:17 -0000 1.22 --- marvin.js 12 Jun 2006 10:51:16 -0000 1.23 *************** *** 381,387 **** --- 381,393 ---- } + function showmol(mol){ + newwin=window.open("nmrshiftdbhtml/showmol.htm","Fenster1","width=310,height=400,left=0,top=0"); + newwin.document.write("<html><body><pre>"+mol+"</pre></body></html>"); + } + function msketch_end() { applet_end(); + document.write("<br><a href=\"javascript:showmol(document."+msketch_name+".getMolFile())\">Show editor content as mol file</a>"); msketch_name = ""; } |
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/html In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv2554/src/html Modified Files: jchempaint-applet-Jama.jar jchempaint-applet-com_ozten.jar jchempaint-applet-core.jar jchempaint-applet-editor-opts.jar jchempaint-applet-editor.jar jchempaint-applet-jas.jar jchempaint-applet-javax_media.jar jchempaint-applet-javax_vecmath.jar jchempaint-applet-nu.jar jchempaint-applet-org.jar jchempaint-applet-org_3pq.jar jchempaint-applet-org_apache.jar jchempaint-applet-org_omegahat.jar jchempaint-applet-org_openscience.jar jchempaint-applet-org_openscience_cdk.jar jchempaint-applet-org_openscience_cdk_applications.jar jchempaint-applet-org_openscience_cdk_applications_jchempaint.jar jchempaint-applet-org_openscience_cdk_config.jar jchempaint-applet-org_openscience_cdk_dict.jar jchempaint-applet-org_openscience_cdk_io.jar jchempaint-applet-org_openscience_cdk_iupac.jar jchempaint-applet-org_openscience_cdk_math.jar jchempaint-applet-org_openscience_cdk_nonotify.jar jchempaint-applet-org_openscience_cdk_qsar.jar jchempaint-applet-org_openscience_cdk_structgen.jar jchempaint-applet-org_openscience_cdk_tools.jar jchempaint-applet-org_w3c.jar jchempaint-applet-org_xmlcml.jar jchempaint-applet-others.jar jchempaint-applet-resources.jar jchempaint-applet-viewer-opts.jar Log Message: new applet Index: jchempaint-applet-Jama.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-Jama.jar,v retrieving revision 1.15 retrieving revision 1.16 diff -C2 -r1.15 -r1.16 Binary files /tmp/cvszd3cO8 and /tmp/cvsoIMaC1 differ Index: jchempaint-applet-com_ozten.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-com_ozten.jar,v retrieving revision 1.15 retrieving revision 1.16 diff -C2 -r1.15 -r1.16 Binary files /tmp/cvsOJHpWa and /tmp/cvs2Qh9N3 differ Index: jchempaint-applet-core.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-core.jar,v retrieving revision 1.44 retrieving revision 1.45 diff -C2 -r1.44 -r1.45 Binary files /tmp/cvsOeElMe and /tmp/cvsxa71H7 differ Index: jchempaint-applet-editor-opts.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-editor-opts.jar,v retrieving revision 1.42 retrieving revision 1.43 diff -C2 -r1.42 -r1.43 Binary files /tmp/cvsyRyJ7e and /tmp/cvsJEo867 differ Index: jchempaint-applet-editor.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-editor.jar,v retrieving revision 1.45 retrieving revision 1.46 diff -C2 -r1.45 -r1.46 Binary files /tmp/cvsDjRBjh and /tmp/cvs6KbGma differ Index: jchempaint-applet-jas.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-jas.jar,v retrieving revision 1.15 retrieving revision 1.16 diff -C2 -r1.15 -r1.16 Binary files /tmp/cvsmL0dGl and /tmp/cvsVp9ILe differ Index: jchempaint-applet-javax_media.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-javax_media.jar,v retrieving revision 1.15 retrieving revision 1.16 diff -C2 -r1.15 -r1.16 Binary files /tmp/cvs1yJhFk and /tmp/cvsMl1COd differ Index: jchempaint-applet-javax_vecmath.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-javax_vecmath.jar,v retrieving revision 1.15 retrieving revision 1.16 diff -C2 -r1.15 -r1.16 Binary files /tmp/cvsFi3rIp and /tmp/cvsx7dQUi differ Index: jchempaint-applet-nu.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-nu.jar,v retrieving revision 1.15 retrieving revision 1.16 diff -C2 -r1.15 -r1.16 Binary files /tmp/cvsy1qoRo and /tmp/cvsHDj36h differ Index: jchempaint-applet-org.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org.jar,v retrieving revision 1.41 retrieving revision 1.42 diff -C2 -r1.41 -r1.42 Binary files /tmp/cvsV9rX7q and /tmp/cvsY1y3qk differ Index: jchempaint-applet-org_3pq.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_3pq.jar,v retrieving revision 1.15 retrieving revision 1.16 diff -C2 -r1.15 -r1.16 Binary files /tmp/cvsX9Qblt and /tmp/cvsjIUEHm differ Index: jchempaint-applet-org_apache.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_apache.jar,v retrieving revision 1.15 retrieving revision 1.16 diff -C2 -r1.15 -r1.16 Binary files /tmp/cvsGjxzbx and /tmp/cvsPiL3Fq differ Index: jchempaint-applet-org_omegahat.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_omegahat.jar,v retrieving revision 1.15 retrieving revision 1.16 diff -C2 -r1.15 -r1.16 Binary files /tmp/cvs2BOcZA and /tmp/cvsl0YNAu differ Index: jchempaint-applet-org_openscience.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience.jar,v retrieving revision 1.41 retrieving revision 1.42 diff -C2 -r1.41 -r1.42 Binary files /tmp/cvsyR6D1G and /tmp/cvsCeuCGA differ Index: jchempaint-applet-org_openscience_cdk.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk.jar,v retrieving revision 1.41 retrieving revision 1.42 diff -C2 -r1.41 -r1.42 Binary files /tmp/cvsjhdJ0F and /tmp/cvsSwHrJz differ Index: jchempaint-applet-org_openscience_cdk_applications.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_applications.jar,v retrieving revision 1.41 retrieving revision 1.42 diff -C2 -r1.41 -r1.42 Binary files /tmp/cvsbO19oI and /tmp/cvs3nyRaC differ Index: jchempaint-applet-org_openscience_cdk_applications_jchempaint.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_applications_jchempaint.jar,v retrieving revision 1.45 retrieving revision 1.46 diff -C2 -r1.45 -r1.46 Binary files /tmp/cvsK14DtM and /tmp/cvsAGNoiG differ Index: jchempaint-applet-org_openscience_cdk_config.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_config.jar,v retrieving revision 1.14 retrieving revision 1.15 diff -C2 -r1.14 -r1.15 Binary files /tmp/cvsplN0bO and /tmp/cvsNHP02H differ Index: jchempaint-applet-org_openscience_cdk_dict.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_dict.jar,v retrieving revision 1.14 retrieving revision 1.15 diff -C2 -r1.14 -r1.15 Binary files /tmp/cvsY1cW9M and /tmp/cvsINyX2G differ Index: jchempaint-applet-org_openscience_cdk_io.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_io.jar,v retrieving revision 1.14 retrieving revision 1.15 diff -C2 -r1.14 -r1.15 Binary files 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retrieving revision 1.3 diff -C2 -r1.2 -r1.3 Binary files /tmp/cvs6UXnpX and /tmp/cvsoK7JvR differ Index: jchempaint-applet-org_openscience_cdk_qsar.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_qsar.jar,v retrieving revision 1.14 retrieving revision 1.15 diff -C2 -r1.14 -r1.15 Binary files /tmp/cvsFNcvzW and /tmp/cvs8FXmJQ differ Index: jchempaint-applet-org_openscience_cdk_structgen.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_structgen.jar,v retrieving revision 1.14 retrieving revision 1.15 diff -C2 -r1.14 -r1.15 Binary files /tmp/cvsO7yETY and /tmp/cvsjUzh6S differ Index: jchempaint-applet-org_openscience_cdk_tools.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_tools.jar,v retrieving revision 1.14 retrieving revision 1.15 diff -C2 -r1.14 -r1.15 Binary files /tmp/cvsxJkKC2 and /tmp/cvs90M4RW differ Index: jchempaint-applet-org_w3c.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_w3c.jar,v retrieving revision 1.15 retrieving revision 1.16 diff -C2 -r1.15 -r1.16 Binary files /tmp/cvs2lfj31 and /tmp/cvs2cxTkW differ Index: jchempaint-applet-org_xmlcml.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_xmlcml.jar,v retrieving revision 1.15 retrieving revision 1.16 diff -C2 -r1.15 -r1.16 Binary files /tmp/cvsMFXfy5 and /tmp/cvs4PqJXZ differ Index: jchempaint-applet-others.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-others.jar,v retrieving revision 1.45 retrieving revision 1.46 diff -C2 -r1.45 -r1.46 Binary files /tmp/cvs57toc9 and /tmp/cvsAt4OW3 differ Index: jchempaint-applet-resources.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-resources.jar,v retrieving revision 1.42 retrieving revision 1.43 diff -C2 -r1.42 -r1.43 Binary files /tmp/cvsTON9Hj and /tmp/cvsGczqJe differ Index: jchempaint-applet-viewer-opts.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-viewer-opts.jar,v retrieving revision 1.41 retrieving revision 1.42 diff -C2 -r1.41 -r1.42 Binary files /tmp/cvssC00gn and /tmp/cvsC1s5ji differ |
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From: Stefan K. <sh...@us...> - 2006-06-09 19:43:07
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv28634/src/vmtemplates Modified Files: details.vm Log Message: spectra displayed together for easy comparision Index: details.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/details.vm,v retrieving revision 1.151 retrieving revision 1.152 diff -C2 -r1.151 -r1.152 *** details.vm 1 Jun 2006 16:01:22 -0000 1.151 --- details.vm 9 Jun 2006 19:42:56 -0000 1.152 *************** *** 176,179 **** --- 176,182 ---- <th><div style="color:white">Intensity</div></th> #end + #if($spectrum.getOtherSpectraStringSize()>0) + <th rowspan="$spectrum.getOtherSpectraStringSize()"><div style="color:white">Other spectra for that structure and spectrum type</div></th> + #end </tr> #end *************** *** 208,211 **** --- 211,215 ---- <td>$option.getIntensity()</td> #end + $spectrum.getOtherSpectraString($option.getValue().intValue()) </tr> #end |
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From: Stefan K. <sh...@us...> - 2006-06-09 19:43:06
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv28634/src/java/org/openscience/nmrshiftdb/om Modified Files: DBSpectrum.java Log Message: spectra displayed together for easy comparision Index: DBSpectrum.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/DBSpectrum.java,v retrieving revision 1.172 retrieving revision 1.173 diff -C2 -r1.172 -r1.173 *** DBSpectrum.java 8 Jun 2006 12:22:45 -0000 1.172 --- DBSpectrum.java 9 Jun 2006 19:42:56 -0000 1.173 *************** *** 1381,1387 **** Vector signals=atoms[i].getDBSignals(this); for(int k=0;k<signals.size();k++){ - Object oo=signals.get(k); - Object o=atoms[i]; - Vector connatoms=atoms[i].getConnectedAtoms(cdkmol,atoms); appletstring.append("S("+((DBSignal)signals.get(k)).getIntensity()+","+atoms[i].getIntegralStuff(atoms, cdkmol)+","+(atoms[i].getSymbol().equals("H") ? getMdlNumberPlus1(((DBAtom)atoms[i].getConnectedAtoms(cdkmol,atoms).get(0)),atoms) : (i+1))+","+((DBSignal)signals.get(k)).getMultiplicity()+")="+((DBSignal)signals.get(k)).getFirstShift().getValue()+"|"); } --- 1381,1384 ---- *************** *** 1389,1392 **** --- 1386,1480 ---- return(appletstring.substring(0,appletstring.length()-2)); } + + + public String getOtherSpectraString(int atomNumber) throws Exception{ + DBAtom assignedTo=this.getDBMolecule().getAtomAt(atomNumber); + StringBuffer sb=new StringBuffer(); + Criteria crit=new Criteria(); + crit.addOrderByColumn(DBSpectrumPeer.SPECTRUM_ID); + crit.add(DBSpectrumPeer.REVIEW_FLAG,"true"); + Vector spectra=this.getDBMolecule().getDBSpectrums(crit); + for(int i=0;i<spectra.size();i++){ + DBSpectrum spectrum=(DBSpectrum)spectra.get(i); + if(!spectrum.getSpectrumId().equals(this.getSpectrumId()) && spectrum.getSpectrumTypeId().equals(this.getSpectrumTypeId())){ + if(this.getDBSpectrumType().getDBIsotope(1).getElementSymbol().equals("H")){ + Vector connatoms=assignedTo.getConnectedAtoms(); + int connhs=0; + for(int k=0;k<connatoms.size();k++){ + if(((DBAtom)connatoms.get(k)).getSymbol().equals("H")){ + connhs++; + } + } + if(connhs==2){ + for(int k=0;k<connatoms.size();k++){ + if(((DBAtom)connatoms.get(k)).getSymbol().equals("H")){ + Criteria crit2=new Criteria(); + crit2.addJoin(DBSignalDBAtomPeer.SIGNAL_ID,DBSignalPeer.SIGNAL_ID); + crit2.add(DBSignalDBAtomPeer.ATOM_ID,((DBAtom)connatoms.get(k)).getAtomId()); + crit2.add(DBSignalPeer.SPECTRUM_ID,spectrum.getSpectrumId()); + Vector v=DBSignalPeer.doSelect(crit2); + if(v.size()>0){ + DBSignal signal=(DBSignal)v.get(0); + sb.append("<td>"+signal.getFirstShift().getValue()+"</td>"); + break; + } + } + } + }else{ + for(int k=0;k<connatoms.size();k++){ + if(((DBAtom)connatoms.get(k)).getSymbol().equals("H")){ + Criteria crit2=new Criteria(); + crit2.addJoin(DBSignalDBAtomPeer.SIGNAL_ID,DBSignalPeer.SIGNAL_ID); + crit2.add(DBSignalDBAtomPeer.ATOM_ID,((DBAtom)connatoms.get(k)).getAtomId()); + crit2.add(DBSignalPeer.SPECTRUM_ID,spectrum.getSpectrumId()); + Vector v=DBSignalPeer.doSelect(crit2); + if(v.size()>0){ + DBSignal signal=(DBSignal)v.get(0); + sb.append("<td>"+signal.getFirstShift().getValue()+"</td>"); + break; + } + } + } + } + }else{ + Criteria crit2=new Criteria(); + crit2.addJoin(DBSignalDBAtomPeer.SIGNAL_ID,DBSignalPeer.SIGNAL_ID); + crit2.add(DBSignalDBAtomPeer.ATOM_ID,assignedTo.getAtomId()); + crit2.add(DBSignalPeer.SPECTRUM_ID,spectrum.getSpectrumId()); + DBSignal signal=(DBSignal)DBSignalPeer.doSelect(crit2).get(0); + sb.append("<td>"+signal.getFirstShift().getValue()+"</td>"); + } + } + } + return sb.toString(); + } + public int getOtherSpectraStringSize() throws Exception{ + StringBuffer sb=new StringBuffer(); + Criteria crit=new Criteria(); + crit.add(DBSpectrumPeer.REVIEW_FLAG,"true"); + crit.add(DBSpectrumPeer.MOLECULE_ID,this.getMoleculeId()); + crit.add(DBSpectrumPeer.SPECTRUM_TYPE_ID, this.getSpectrumTypeId()); + crit.add(DBSpectrumPeer.SPECTRUM_ID,this.getSpectrumId(),Criteria.NOT_EQUAL); + Vector spectra=this.getDBMolecule().getDBSpectrums(crit); + System.err.println(spectra.size()); + System.err.println(spectra.size()); + System.err.println(spectra.size()); + System.err.println(spectra.size()); + System.err.println(spectra.size()); + System.err.println(spectra.size()); + System.err.println(spectra.size()); + System.err.println(spectra.size()); + System.err.println(spectra.size()); + System.err.println(spectra.size()); + System.err.println(spectra.size()); + System.err.println(spectra.size()); + System.err.println(spectra.size()); + System.err.println(spectra.size()); + System.err.println(spectra.size()); + System.err.println(spectra.size()); + System.err.println(spectra.size()); + System.err.println(spectra.size()); + return(spectra.size()); + } } |
