From: <ni...@us...> - 2008-10-11 14:27:13
|
Revision: 10050 http://jmol.svn.sourceforge.net/jmol/?rev=10050&view=rev Author: nicove Date: 2008-10-11 14:26:52 +0000 (Sat, 11 Oct 2008) Log Message: ----------- Adding Amber files to fah page Modified Paths: -------------- trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java Added Paths: ----------- trunk/Jmol-FAH/projects/p4606.top.gz trunk/Jmol-FAH/projects/p4606.trj.gz Property changes on: trunk/Jmol-FAH/projects/p4606.top.gz ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Property changes on: trunk/Jmol-FAH/projects/p4606.trj.gz ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Modified: trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java =================================================================== --- trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java 2008-10-11 13:57:35 UTC (rev 10049) +++ trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java 2008-10-11 14:26:52 UTC (rev 10050) @@ -1245,6 +1245,25 @@ if (separator) { outputNewLine(); } + separator = false; + for (int ii = 0; ii < _projectInfo.size(); ii++) { + Information info = getInfo(ii); + if (info != null) { + if ((info._psName != null) && + ((info._staticFile == null) || (!info._staticFile.contains("top")))) { + if (info._staticCore == CoreType.AMBER) { + if (!separator) { + outputText("Active missing amber beta projects: "); + } + outputInfo("", "p" + ii, separator); + separator = true; + } + } + } + } + if (separator) { + outputNewLine(); + } // Public projects separator = false; @@ -1267,6 +1286,26 @@ if (separator) { outputNewLine(); } + separator = false; + for (int ii = 0; ii < _projectInfo.size(); ii++) { + Information info = getInfo(ii); + if (info != null) { + if ((info._psName != null) && + ((info._staticFile == null) || (!info._staticFile.contains("top"))) && + (Boolean.TRUE.equals(info._staticPublic))) { + if (info._staticCore == CoreType.AMBER) { + if (!separator) { + outputText("Active missing amber public projects: "); + } + outputInfo("", "p" + ii, separator); + separator = true; + } + } + } + } + if (separator) { + outputNewLine(); + } } /** @@ -1278,7 +1317,7 @@ // Get project informations Information info = getInfo(projectNumber); - // Check for file + // Check for xyz file StringBuffer filePath = new StringBuffer(); filePath.append("./projects/p"); //$NON-NLS-1$ filePath.append(projectNumber); @@ -1298,6 +1337,27 @@ projectNumber); } } + + // Check for amber file + filePath.setLength(0); + filePath.append("./projects/p"); //$NON-NLS-1$ + filePath.append(projectNumber); + filePath.append(".top.gz"); //$NON-NLS-1$ + file = new File(filePath.toString()); + + if (file.exists()) { + if ((info == null) || ((info._staticFile == null) || (!info._staticFile.contains("top")))) { + System.out.println( + "Missing top file in XML file for project " + //$NON-NLS-1$ + projectNumber); + } + } else { + if ((info != null) && ((info._staticFile != null) && (info._staticFile.contains("top")))) { + System.out.println( + "Missing top file for project " + //$NON-NLS-1$ + projectNumber); + } + } } /** This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2008-10-20 19:30:17
|
Revision: 10125 http://jmol.svn.sourceforge.net/jmol/?rev=10125&view=rev Author: nicove Date: 2008-10-20 19:30:09 +0000 (Mon, 20 Oct 2008) Log Message: ----------- Folding@Home Modified Paths: -------------- trunk/Jmol-FAH/src/org/jmol/fah/CoreType.java Added Paths: ----------- trunk/Jmol-FAH/projects/p2170.top.gz trunk/Jmol-FAH/projects/p2170.trj.gz trunk/Jmol-FAH/projects/p2494.xyz.gz trunk/Jmol-FAH/projects/p2670.xyz.gz trunk/Jmol-FAH/projects/p4600.top.gz trunk/Jmol-FAH/projects/p4600.trj.gz Added: trunk/Jmol-FAH/projects/p2170.top.gz =================================================================== (Binary files differ) Property changes on: trunk/Jmol-FAH/projects/p2170.top.gz ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: trunk/Jmol-FAH/projects/p2170.trj.gz =================================================================== (Binary files differ) Property changes on: trunk/Jmol-FAH/projects/p2170.trj.gz ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: trunk/Jmol-FAH/projects/p2494.xyz.gz =================================================================== (Binary files differ) Property changes on: trunk/Jmol-FAH/projects/p2494.xyz.gz ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: trunk/Jmol-FAH/projects/p2670.xyz.gz =================================================================== (Binary files differ) Property changes on: trunk/Jmol-FAH/projects/p2670.xyz.gz ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: trunk/Jmol-FAH/projects/p4600.top.gz =================================================================== (Binary files differ) Property changes on: trunk/Jmol-FAH/projects/p4600.top.gz ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: trunk/Jmol-FAH/projects/p4600.trj.gz =================================================================== (Binary files differ) Property changes on: trunk/Jmol-FAH/projects/p4600.trj.gz ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Modified: trunk/Jmol-FAH/src/org/jmol/fah/CoreType.java =================================================================== --- trunk/Jmol-FAH/src/org/jmol/fah/CoreType.java 2008-10-20 03:26:23 UTC (rev 10124) +++ trunk/Jmol-FAH/src/org/jmol/fah/CoreType.java 2008-10-20 19:30:09 UTC (rev 10125) @@ -198,7 +198,7 @@ static public final CoreType DGROMACSB = new CoreType("DGromacsB", "DB", true); //$NON-NLS-1$ //$NON-NLS-2$ static public final CoreType DGROMACSC = new CoreType("DGromacsC", "DC", true); //$NON-NLS-1$ //$NON-NLS-2$ static public final CoreType GBGROMACS = new CoreType("GBGromacs", "GB", true); //$NON-NLS-1$ //$NON-NLS-2$ - static public final CoreType GROCVS = new CoreType("GroCVS", "GC", false); //$NON-NLS-1$ //$NON-NLS-2$ + static public final CoreType GROCVS = new CoreType("GroCVS", "GC", true); //$NON-NLS-1$ //$NON-NLS-2$ static public final CoreType GROGPU = new CoreType("GroGPU", "GG", false); //$NON-NLS-1$ //$NON-NLS-2$ static public final CoreType GROGPU2 = new CoreType("GroGPU2", "GG2", false); //$NON-NLS-1$ //$NON-NLS-2$ static public final CoreType GROMACS = new CoreType("Gromacs", "G", true); //$NON-NLS-1$ //$NON-NLS-2$ This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2008-11-01 10:33:34
|
Revision: 10193 http://jmol.svn.sourceforge.net/jmol/?rev=10193&view=rev Author: nicove Date: 2008-11-01 10:33:30 +0000 (Sat, 01 Nov 2008) Log Message: ----------- Folding@Home Modified Paths: -------------- trunk/Jmol-FAH/.classpath trunk/Jmol-FAH/build.xml trunk/Jmol-FAH/jars/activation/LICENSE_activation.txt trunk/Jmol-FAH/jars/activation/activation.jar trunk/Jmol-FAH/jars/mail/LICENSE_mail.txt trunk/Jmol-FAH/jars/mail/mail.jar trunk/Jmol-FAH/src/org/jmol/fah/Jmol-FAH.properties trunk/Jmol-FAH/src/org/jmol/fah/checkxyz/Configuration.java trunk/Jmol-FAH/src/org/jmol/fah/checkxyz/ConfigurationWindow.java trunk/Jmol-FAH/src/org/jmol/fah/checkxyz/MailSender.java Added Paths: ----------- trunk/Jmol-FAH/jars/commons-email/commons-email-1.1.jar Removed Paths: ------------- trunk/Jmol-FAH/jars/commons-email/commons-email-1.0.jar Modified: trunk/Jmol-FAH/.classpath =================================================================== --- trunk/Jmol-FAH/.classpath 2008-10-31 23:06:17 UTC (rev 10192) +++ trunk/Jmol-FAH/.classpath 2008-11-01 10:33:30 UTC (rev 10193) @@ -2,8 +2,8 @@ <classpath> <classpathentry kind="src" path="src"/> <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/> - <classpathentry kind="lib" path="jars/commons-email/commons-email-1.0.jar"/> <classpathentry kind="lib" path="jars/mail/mail.jar"/> <classpathentry kind="lib" path="jars/activation/activation.jar"/> + <classpathentry kind="lib" path="jars/commons-email/commons-email-1.1.jar"/> <classpathentry kind="output" path="bin"/> </classpath> Modified: trunk/Jmol-FAH/build.xml =================================================================== --- trunk/Jmol-FAH/build.xml 2008-10-31 23:06:17 UTC (rev 10192) +++ trunk/Jmol-FAH/build.xml 2008-11-01 10:33:30 UTC (rev 10193) @@ -17,7 +17,7 @@ <property name="activation.jar" value="activation.jar" /> <property name="activation.lic" value="LICENSE_activation.txt" /> <property name="commons-email.dir" value="jars/commons-email" /> - <property name="commons-email.jar" value="commons-email-1.0.jar" /> + <property name="commons-email.jar" value="commons-email-1.1.jar" /> <property name="commons-email.lic" value="LICENSE_commonsemail.txt" /> <property name="mail.dir" value="jars/mail" /> <property name="mail.jar" value="mail.jar" /> Modified: trunk/Jmol-FAH/jars/activation/LICENSE_activation.txt =================================================================== --- trunk/Jmol-FAH/jars/activation/LICENSE_activation.txt 2008-10-31 23:06:17 UTC (rev 10192) +++ trunk/Jmol-FAH/jars/activation/LICENSE_activation.txt 2008-11-01 10:33:30 UTC (rev 10193) @@ -4,7 +4,7 @@ Effective Date: Date of delivery of the Software to You. -Software: JavaBeans Activation Framework 1.1. +Software: JavaBeans Activation Framework 1.1.1. License Term: Perpetual (subject to termination under the SLA). Modified: trunk/Jmol-FAH/jars/activation/activation.jar =================================================================== (Binary files differ) Deleted: trunk/Jmol-FAH/jars/commons-email/commons-email-1.0.jar =================================================================== (Binary files differ) Added: trunk/Jmol-FAH/jars/commons-email/commons-email-1.1.jar =================================================================== (Binary files differ) Property changes on: trunk/Jmol-FAH/jars/commons-email/commons-email-1.1.jar ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Modified: trunk/Jmol-FAH/jars/mail/LICENSE_mail.txt =================================================================== --- trunk/Jmol-FAH/jars/mail/LICENSE_mail.txt 2008-10-31 23:06:17 UTC (rev 10192) +++ trunk/Jmol-FAH/jars/mail/LICENSE_mail.txt 2008-11-01 10:33:30 UTC (rev 10193) @@ -4,7 +4,7 @@ Effective Date: Date of delivery of the Software to You. -Software: JavaMail 1.4. +Software: JavaMail 1.4.1. License Term: Perpetual (subject to termination under the SLA). Modified: trunk/Jmol-FAH/jars/mail/mail.jar =================================================================== (Binary files differ) Modified: trunk/Jmol-FAH/src/org/jmol/fah/Jmol-FAH.properties =================================================================== --- trunk/Jmol-FAH/src/org/jmol/fah/Jmol-FAH.properties 2008-10-31 23:06:17 UTC (rev 10192) +++ trunk/Jmol-FAH/src/org/jmol/fah/Jmol-FAH.properties 2008-11-01 10:33:30 UTC (rev 10193) @@ -3,4 +3,4 @@ # # Version # -Version=0.4 +Version=0.5 Modified: trunk/Jmol-FAH/src/org/jmol/fah/checkxyz/Configuration.java =================================================================== --- trunk/Jmol-FAH/src/org/jmol/fah/checkxyz/Configuration.java 2008-10-31 23:06:17 UTC (rev 10192) +++ trunk/Jmol-FAH/src/org/jmol/fah/checkxyz/Configuration.java 2008-11-01 10:33:30 UTC (rev 10193) @@ -41,6 +41,7 @@ private String userName; private String mailServer; + private int mailPort; private String userMail; private String login; private String password; @@ -55,6 +56,7 @@ public Configuration() { userName = ""; mailServer = ""; + mailPort = 25; userMail = ""; login = ""; password = ""; @@ -76,6 +78,12 @@ userName = props.getProperty("userName", userName); mailServer = props.getProperty("mailServer", mailServer); + String txtPort = props.getProperty("mailPort", Integer.toString(mailPort)); + try { + mailPort = Integer.parseInt(txtPort); + } catch (NumberFormatException e) { + mailPort = 25; + } userMail = props.getProperty("userMail", userMail); login = props.getProperty("login", login); password = props.getProperty("password", password); @@ -105,6 +113,7 @@ Properties props = new Properties(); props.setProperty("userName", userName); props.setProperty("mailServer", mailServer); + props.setProperty("mailPort", Integer.toString(mailPort)); props.setProperty("userMail", userMail); props.setProperty("login", login); props.setProperty("password", password); @@ -171,6 +180,16 @@ } /** + * @param port Mail port. + */ + public void setMailPort(int port) { + mailPort = port; + } + public int getMailPort() { + return mailPort; + } + + /** * @param address User mail address. */ public void setUserMail(String address) { Modified: trunk/Jmol-FAH/src/org/jmol/fah/checkxyz/ConfigurationWindow.java =================================================================== --- trunk/Jmol-FAH/src/org/jmol/fah/checkxyz/ConfigurationWindow.java 2008-10-31 23:06:17 UTC (rev 10192) +++ trunk/Jmol-FAH/src/org/jmol/fah/checkxyz/ConfigurationWindow.java 2008-11-01 10:33:30 UTC (rev 10193) @@ -33,6 +33,8 @@ import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.io.File; +import java.text.NumberFormat; +import java.text.ParseException; import java.util.Iterator; import java.util.Vector; @@ -41,6 +43,7 @@ import javax.swing.JButton; import javax.swing.JComponent; import javax.swing.JFileChooser; +import javax.swing.JFormattedTextField; import javax.swing.JFrame; import javax.swing.JLabel; import javax.swing.JList; @@ -66,6 +69,7 @@ private JTextField textUser = null; private JTextField textMailServer = null; + private JFormattedTextField textMailPort = null; private JTextField textUserMail = null; private JTextField textUserLogin = null; private JTextField textUserPassword = null; @@ -218,6 +222,26 @@ constraints.gridy++; + // Mail port + JLabel labelMailPort = new JLabel("Mail port : ", SwingConstants.RIGHT); + constraints.gridx = 0; + constraints.weightx = 0; + constraints.anchor = GridBagConstraints.EAST; + panel.add(labelMailPort, constraints); + + NumberFormat portFormat = NumberFormat.getIntegerInstance(); + portFormat.setMaximumFractionDigits(0); + portFormat.setMaximumIntegerDigits(5); + textMailPort = new JFormattedTextField(portFormat); + textMailPort.setColumns(15); + textMailPort.setToolTipText("Your mail server port, usually 25"); + textMailPort.setValue(Integer.valueOf(configuration.getMailPort())); + constraints.gridx++; + constraints.weightx = 1; + constraints.anchor = GridBagConstraints.WEST; + panel.add(textMailPort, constraints); + + constraints.gridy++; // User mail JLabel labelUserMail = new JLabel("Mail address :", SwingConstants.RIGHT); constraints.gridx = 0; @@ -380,9 +404,22 @@ public void actionPerformed(ActionEvent e) { if (actionOk.equals(e.getActionCommand())) { + // Check Port value + try { + textMailPort.commitEdit(); + } catch (ParseException ex) { + JOptionPane.showMessageDialog( + this, "The mail port value is incorrect.", "Incorrect value", JOptionPane.ERROR_MESSAGE); + return; + } // Validate configuration configuration.setUserName(textUser.getText()); configuration.setMailServer(textMailServer.getText()); + Object portValue = textMailPort.getValue(); + if (portValue instanceof Integer) { + Integer port = (Integer) portValue; + configuration.setMailPort(port.intValue()); + } configuration.setUserMail(textUserMail.getText()); configuration.setLogin(textUserLogin.getText()); configuration.setPassword(textUserPassword.getText()); @@ -443,6 +480,15 @@ } else if (actionTestMail.equals(e.getActionCommand())) { + // Check Port value + try { + textMailPort.commitEdit(); + } catch (ParseException ex) { + JOptionPane.showMessageDialog( + this, "The mail port value is incorrect.", "Incorrect value", JOptionPane.ERROR_MESSAGE); + return; + } + // Test mail configuration JFileChooser fileChooser = new JFileChooser(); fileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY); @@ -456,12 +502,18 @@ Configuration config = new Configuration(); config.setLogin(textUserLogin.getText()); config.setMailServer(textMailServer.getText()); + Object portValue = textMailPort.getValue(); + if (portValue instanceof Long) { + Long port = (Long) portValue; + config.setMailPort(port.intValue()); + } config.setPassword(textUserPassword.getText()); config.setUserMail(textUserMail.getText()); config.setUserName(textUser.getText()); File[] files = new File[1]; files[0] = testFile; MailSender sender = new MailSender(config, "XXXX", files, true); + setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); try { sender.sendMail(); JOptionPane.showMessageDialog( @@ -475,6 +527,7 @@ "Error while sending mail", JOptionPane.ERROR_MESSAGE); } + setCursor(Cursor.getDefaultCursor()); } } Modified: trunk/Jmol-FAH/src/org/jmol/fah/checkxyz/MailSender.java =================================================================== --- trunk/Jmol-FAH/src/org/jmol/fah/checkxyz/MailSender.java 2008-10-31 23:06:17 UTC (rev 10192) +++ trunk/Jmol-FAH/src/org/jmol/fah/checkxyz/MailSender.java 2008-11-01 10:33:30 UTC (rev 10193) @@ -73,6 +73,7 @@ // Create the mail MultiPartEmail email = new MultiPartEmail(); email.setHostName(config.getMailServer()); + email.setSmtpPort(config.getMailPort()); if (testing) { email.addTo(config.getUserMail(), config.getUserName()); } else { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2008-11-02 17:43:30
|
Revision: 10224 http://jmol.svn.sourceforge.net/jmol/?rev=10224&view=rev Author: nicove Date: 2008-11-02 17:43:26 +0000 (Sun, 02 Nov 2008) Log Message: ----------- Findbugs Modified Paths: -------------- trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java trunk/Jmol-FAH/src/org/jmol/fah/checkxyz/Check.java trunk/Jmol-FAH/src/org/jmol/fah/checkxyz/Configuration.java Added Paths: ----------- trunk/Jmol-FAH/.fbprefs trunk/Jmol-FAH/FindbugsExclude.xml Property Changed: ---------------- trunk/Jmol-FAH/ Property changes on: trunk/Jmol-FAH ___________________________________________________________________ Modified: svn:ignore - bin ProjectInfo.txt build fci-data.xml + bin ProjectInfo.txt build fci-data.xml Added: trunk/Jmol-FAH/.fbprefs =================================================================== --- trunk/Jmol-FAH/.fbprefs (rev 0) +++ trunk/Jmol-FAH/.fbprefs 2008-11-02 17:43:26 UTC (rev 10224) @@ -0,0 +1,157 @@ +#FindBugs User Preferences +#Sun Nov 02 18:32:58 CET 2008 +detectorAppendingToAnObjectOutputStream=AppendingToAnObjectOutputStream|true +detectorBCPMethodReturnCheck=BCPMethodReturnCheck|false +detectorBadAppletConstructor=BadAppletConstructor|false +detectorBadResultSetAccess=BadResultSetAccess|true +detectorBadSyntaxForRegularExpression=BadSyntaxForRegularExpression|true +detectorBadUseOfReturnValue=BadUseOfReturnValue|true +detectorBadlyOverriddenAdapter=BadlyOverriddenAdapter|true +detectorBooleanReturnNull=BooleanReturnNull|true +detectorBuildInterproceduralCallGraph=BuildInterproceduralCallGraph|false +detectorBuildObligationPolicyDatabase=BuildObligationPolicyDatabase|true +detectorCallToUnsupportedMethod=CallToUnsupportedMethod|true +detectorCalledMethods=CalledMethods|true +detectorCheckCalls=CheckCalls|false +detectorCheckExpectedWarnings=CheckExpectedWarnings|false +detectorCheckImmutableAnnotation=CheckImmutableAnnotation|true +detectorCheckTypeQualifiers=CheckTypeQualifiers|true +detectorCloneIdiom=CloneIdiom|true +detectorComparatorIdiom=ComparatorIdiom|true +detectorConfusedInheritance=ConfusedInheritance|true +detectorConfusionBetweenInheritedAndOuterMethod=ConfusionBetweenInheritedAndOuterMethod|true +detectorCrossSiteScripting=CrossSiteScripting|true +detectorDoInsideDoPrivileged=DoInsideDoPrivileged|true +detectorDontCatchIllegalMonitorStateException=DontCatchIllegalMonitorStateException|true +detectorDontUseEnum=DontUseEnum|true +detectorDroppedException=DroppedException|true +detectorDumbMethodInvocations=DumbMethodInvocations|true +detectorDumbMethods=DumbMethods|true +detectorDuplicateBranches=DuplicateBranches|true +detectorEmptyZipFileEntry=EmptyZipFileEntry|true +detectorEqStringTest=EqStringTest|false +detectorEqualsOperandShouldHaveClassCompatibleWithThis=EqualsOperandShouldHaveClassCompatibleWithThis|true +detectorFieldItemSummary=FieldItemSummary|true +detectorFinalizerNullsFields=FinalizerNullsFields|true +detectorFindBadCast=FindBadCast|false +detectorFindBadCast2=FindBadCast2|true +detectorFindBadEqualsImplementation=FindBadEqualsImplementation|false +detectorFindBadForLoop=FindBadForLoop|true +detectorFindBugsSummaryStats=FindBugsSummaryStats|true +detectorFindCircularDependencies=FindCircularDependencies|false +detectorFindDeadLocalStores=FindDeadLocalStores|true +detectorFindDoubleCheck=FindDoubleCheck|true +detectorFindEmptySynchronizedBlock=FindEmptySynchronizedBlock|true +detectorFindFieldSelfAssignment=FindFieldSelfAssignment|true +detectorFindFinalizeInvocations=FindFinalizeInvocations|true +detectorFindFloatEquality=FindFloatEquality|true +detectorFindFloatMath=FindFloatMath|false +detectorFindHEmismatch=FindHEmismatch|true +detectorFindInconsistentSync2=FindInconsistentSync2|true +detectorFindJSR166LockMonitorenter=FindJSR166LockMonitorenter|true +detectorFindLocalSelfAssignment2=FindLocalSelfAssignment2|true +detectorFindMaskedFields=FindMaskedFields|true +detectorFindMismatchedWaitOrNotify=FindMismatchedWaitOrNotify|true +detectorFindNakedNotify=FindNakedNotify|true +detectorFindNonSerializableStoreIntoSession=FindNonSerializableStoreIntoSession|true +detectorFindNonSerializableValuePassedToWriteObject=FindNonSerializableValuePassedToWriteObject|true +detectorFindNonShortCircuit=FindNonShortCircuit|true +detectorFindNullDeref=FindNullDeref|true +detectorFindNullDerefsInvolvingNonShortCircuitEvaluation=FindNullDerefsInvolvingNonShortCircuitEvaluation|true +detectorFindOpenStream=FindOpenStream|true +detectorFindPuzzlers=FindPuzzlers|true +detectorFindRefComparison=FindRefComparison|true +detectorFindReturnRef=FindReturnRef|true +detectorFindRunInvocations=FindRunInvocations|true +detectorFindSelfComparison=FindSelfComparison|true +detectorFindSelfComparison2=FindSelfComparison2|true +detectorFindSleepWithLockHeld=FindSleepWithLockHeld|true +detectorFindSpinLoop=FindSpinLoop|true +detectorFindSqlInjection=FindSqlInjection|true +detectorFindTwoLockWait=FindTwoLockWait|true +detectorFindUncalledPrivateMethods=FindUncalledPrivateMethods|true +detectorFindUnconditionalWait=FindUnconditionalWait|true +detectorFindUninitializedGet=FindUninitializedGet|true +detectorFindUnrelatedTypesInGenericContainer=FindUnrelatedTypesInGenericContainer|true +detectorFindUnreleasedLock=FindUnreleasedLock|true +detectorFindUnsatisfiedObligation=FindUnsatisfiedObligation|true +detectorFindUnsyncGet=FindUnsyncGet|true +detectorFindUselessControlFlow=FindUselessControlFlow|true +detectorFormatStringChecker=FormatStringChecker|true +detectorHugeSharedStringConstants=HugeSharedStringConstants|true +detectorIDivResultCastToDouble=IDivResultCastToDouble|true +detectorIncompatMask=IncompatMask|true +detectorInconsistentAnnotations=InconsistentAnnotations|true +detectorInefficientMemberAccess=InefficientMemberAccess|false +detectorInefficientToArray=InefficientToArray|true +detectorInfiniteLoop=InfiniteLoop|true +detectorInfiniteRecursiveLoop=InfiniteRecursiveLoop|true +detectorInfiniteRecursiveLoop2=InfiniteRecursiveLoop2|false +detectorInheritanceUnsafeGetResource=InheritanceUnsafeGetResource|true +detectorInitializationChain=InitializationChain|true +detectorInstantiateStaticClass=InstantiateStaticClass|true +detectorInvalidJUnitTest=InvalidJUnitTest|true +detectorIteratorIdioms=IteratorIdioms|true +detectorLazyInit=LazyInit|true +detectorLoadOfKnownNullValue=LoadOfKnownNullValue|true +detectorLockedFields=LockedFields|false +detectorMethodReturnCheck=MethodReturnCheck|true +detectorMethods=Methods|true +detectorMultithreadedInstanceAccess=MultithreadedInstanceAccess|true +detectorMutableLock=MutableLock|true +detectorMutableStaticFields=MutableStaticFields|true +detectorNaming=Naming|true +detectorNoteAnnotationRetention=NoteAnnotationRetention|true +detectorNoteCheckReturnValue=NoteCheckReturnValue|true +detectorNoteCheckReturnValueAnnotations=NoteCheckReturnValueAnnotations|true +detectorNoteDirectlyRelevantTypeQualifiers=NoteDirectlyRelevantTypeQualifiers|true +detectorNoteJCIPAnnotation=NoteJCIPAnnotation|true +detectorNoteNonNullAnnotations=NoteNonNullAnnotations|true +detectorNoteNonnullReturnValues=NoteNonnullReturnValues|true +detectorNoteSuppressedWarnings=NoteSuppressedWarnings|true +detectorNoteUnconditionalParamDerefs=NoteUnconditionalParamDerefs|true +detectorNumberConstructor=NumberConstructor|true +detectorOverridingEqualsNotSymmetrical=OverridingEqualsNotSymmetrical|true +detectorPreferZeroLengthArrays=PreferZeroLengthArrays|true +detectorPublicSemaphores=PublicSemaphores|false +detectorQuestionableBooleanAssignment=QuestionableBooleanAssignment|true +detectorReadReturnShouldBeChecked=ReadReturnShouldBeChecked|true +detectorRedundantInterfaces=RedundantInterfaces|true +detectorReflectiveClasses=ReflectiveClasses|true +detectorRepeatedConditionals=RepeatedConditionals|true +detectorResolveAllReferences=ResolveAllReferences|false +detectorRuntimeExceptionCapture=RuntimeExceptionCapture|true +detectorSerializableIdiom=SerializableIdiom|true +detectorStartInConstructor=StartInConstructor|true +detectorStaticCalendarDetector=StaticCalendarDetector|true +detectorStringConcatenation=StringConcatenation|true +detectorSuperfluousInstanceOf=SuperfluousInstanceOf|true +detectorSuspiciousThreadInterrupted=SuspiciousThreadInterrupted|true +detectorSwitchFallthrough=SwitchFallthrough|true +detectorSynchronizationOnSharedBuiltinConstant=SynchronizationOnSharedBuiltinConstant|true +detectorSynchronizeAndNullCheckField=SynchronizeAndNullCheckField|true +detectorSynchronizeOnClassLiteralNotGetClass=SynchronizeOnClassLiteralNotGetClass|true +detectorSynchronizingOnContentsOfFieldToProtectField=SynchronizingOnContentsOfFieldToProtectField|true +detectorTestASM=TestASM|false +detectorTestDataflowAnalysis=TestDataflowAnalysis|false +detectorTestingGround=TestingGround|false +detectorTrainFieldStoreTypes=TrainFieldStoreTypes|true +detectorTrainNonNullAnnotations=TrainNonNullAnnotations|true +detectorTrainUnconditionalDerefParams=TrainUnconditionalDerefParams|true +detectorURLProblems=URLProblems|true +detectorUncallableMethodOfAnonymousClass=UncallableMethodOfAnonymousClass|true +detectorUnnecessaryMath=UnnecessaryMath|true +detectorUnreadFields=UnreadFields|true +detectorUseObjectEquals=UseObjectEquals|false +detectorUselessSubclassMethod=UselessSubclassMethod|false +detectorVarArgsProblems=VarArgsProblems|true +detectorVolatileUsage=VolatileUsage|true +detectorWaitInLoop=WaitInLoop|true +detectorWrongMapIterator=WrongMapIterator|true +detectorXMLFactoryBypass=XMLFactoryBypass|true +detector_threshold=2 +effort=default +excludefilter0=FindbugsExclude.xml +filter_settings=Medium|BAD_PRACTICE,CORRECTNESS,EXPERIMENTAL,I18N,MALICIOUS_CODE,MT_CORRECTNESS,PERFORMANCE,SECURITY,STYLE|false +filter_settings_neg=| +run_at_full_build=true Added: trunk/Jmol-FAH/FindbugsExclude.xml =================================================================== --- trunk/Jmol-FAH/FindbugsExclude.xml (rev 0) +++ trunk/Jmol-FAH/FindbugsExclude.xml 2008-11-02 17:43:26 UTC (rev 10224) @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<FindBugsFilter> + <!-- Exclude Jmol Fah code --> + <Match> + <Package name="~org\.jmol\.fah.*"/> + <Or> + <Bug pattern="DM_EXIT"/> + <Bug pattern="EI_EXPOSE_REP2"/> + <Bug pattern="NP_BOOLEAN_RETURN_NULL"/> + </Or> + </Match> +</FindBugsFilter> \ No newline at end of file Property changes on: trunk/Jmol-FAH/FindbugsExclude.xml ___________________________________________________________________ Added: svn:mime-type + text/plain Modified: trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java =================================================================== --- trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java 2008-11-02 17:23:12 UTC (rev 10223) +++ trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java 2008-11-02 17:43:26 UTC (rev 10224) @@ -281,8 +281,12 @@ output.close(); // Manage local file - file.delete(); - tmpFile.renameTo(file); + if (!file.delete()) { + System.out.println("Error deleting file " + file.toString()); + } + if (!tmpFile.renameTo(file)) { + System.out.println("Error renaming file " + tmpFile.toString() + " to " + file.toString()); + } System.out.println("File updated"); } catch (IOException e) { System.out.println("Error " + e.getMessage()); @@ -407,6 +411,7 @@ * Add information from psummaryC.html */ private void addPSCInformation() { + Reader reader = null; try { //Check file existence and time long psDate = System.currentTimeMillis(); @@ -439,7 +444,6 @@ } //Load new information - Reader reader = null; if (_local == true) { reader = new FileReader("psummary.html"); //$NON-NLS-1$ } else { @@ -464,6 +468,14 @@ //Empty } catch (BadLocationException e) { //Empty + } finally { + if (reader != null) { + try { + reader.close(); + } catch (IOException e) { + // + } + } } } @@ -471,6 +483,7 @@ * Add information from psummary.html */ private void addPSInformation() { + Reader reader = null; try { //Check file existence and time //long psDate = System.currentTimeMillis(); @@ -479,7 +492,6 @@ } //Load new information - Reader reader = null; if (_local == true) { reader = new FileReader("psummary.html"); //$NON-NLS-1$ } else { @@ -503,6 +515,14 @@ //Empty } catch (BadLocationException e) { //Empty + } finally { + if (reader != null) { + try { + reader.close(); + } catch (IOException e) { + // + } + } } } @@ -607,6 +627,7 @@ DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); factory.setNamespaceAware(true); + InputStream stream = null; try { // Retrieve distant file File localFile = new File("fci-data.xml"); @@ -616,7 +637,7 @@ } //Load document - InputStream stream = new FileInputStream(localFile); + stream = new FileInputStream(localFile); DocumentBuilder builder = factory.newDocumentBuilder(); Document document = builder.parse(stream); @@ -643,6 +664,14 @@ //Empty } catch (IOException e) { //Empty + } finally { + if (stream != null) { + try { + stream.close(); + } catch (IOException e) { + // + } + } } } Modified: trunk/Jmol-FAH/src/org/jmol/fah/checkxyz/Check.java =================================================================== --- trunk/Jmol-FAH/src/org/jmol/fah/checkxyz/Check.java 2008-11-02 17:23:12 UTC (rev 10223) +++ trunk/Jmol-FAH/src/org/jmol/fah/checkxyz/Check.java 2008-11-02 17:43:26 UTC (rev 10224) @@ -84,7 +84,10 @@ } }; File configDirectory = new File(new File(System.getProperty("user.home")), ".jmol"); - configDirectory.mkdirs(); + if (!configDirectory.mkdirs() && + (!configDirectory.exists() || !configDirectory.isDirectory())) { + System.out.println("Error creating directory " + configDirectory.toString()); + } availableProjects = new File(configDirectory, "availableProjects"); availableAmbers = new File(configDirectory, "availableAmbers"); } Modified: trunk/Jmol-FAH/src/org/jmol/fah/checkxyz/Configuration.java =================================================================== --- trunk/Jmol-FAH/src/org/jmol/fah/checkxyz/Configuration.java 2008-11-02 17:23:12 UTC (rev 10223) +++ trunk/Jmol-FAH/src/org/jmol/fah/checkxyz/Configuration.java 2008-11-02 17:43:26 UTC (rev 10224) @@ -74,11 +74,13 @@ * Load configuration from file. */ public void loadConfiguration() { + FileInputStream fis = null; try { - FileInputStream fis = new FileInputStream(configFile); + fis = new FileInputStream(configFile); Properties props = new Properties(); props.load(fis); fis.close(); + fis = null; userName = props.getProperty("userName", userName); mailServer = props.getProperty("mailServer", mailServer); @@ -113,6 +115,14 @@ } } catch (IOException e) { // + } finally { + if (fis != null) { + try { + fis.close(); + } catch (IOException e) { + // + } + } } } @@ -121,6 +131,7 @@ * Save configuration in file. */ public void saveConfiguration() { + FileOutputStream fos = null; try { Properties props = new Properties(); props.setProperty("userName", userName); @@ -143,11 +154,18 @@ props.setProperty("sent_" + num, iter.next().toString()); num++; } - FileOutputStream fos = new FileOutputStream(configFile); + fos = new FileOutputStream(configFile); props.store(fos, "Jmol FAH"); - fos.close(); } catch (IOException e) { // + } finally { + if (fos != null) { + try { + fos.close(); + } catch (IOException e) { + // + } + } } } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2008-11-08 17:21:50
|
Revision: 10267 http://jmol.svn.sourceforge.net/jmol/?rev=10267&view=rev Author: nicove Date: 2008-11-08 17:21:46 +0000 (Sat, 08 Nov 2008) Log Message: ----------- Folding@Home Modified Paths: -------------- trunk/Jmol-FAH/.classpath trunk/Jmol-FAH/build.xml trunk/Jmol-FAH/src/org/jmol/fah/Jmol-FAH.properties trunk/Jmol-FAH/src/org/jmol/fah/checkxyz/Check.java trunk/Jmol-FAH/src/org/jmol/fah/checkxyz/Configuration.java trunk/Jmol-FAH/src/org/jmol/fah/checkxyz/ConfigurationWindow.java Added Paths: ----------- trunk/Jmol-FAH/jars/commons-io/ trunk/Jmol-FAH/jars/commons-io/LICENSE_commonsio.txt trunk/Jmol-FAH/jars/commons-io/commons-io-1.4.jar Modified: trunk/Jmol-FAH/.classpath =================================================================== --- trunk/Jmol-FAH/.classpath 2008-11-08 17:00:07 UTC (rev 10266) +++ trunk/Jmol-FAH/.classpath 2008-11-08 17:21:46 UTC (rev 10267) @@ -5,5 +5,6 @@ <classpathentry kind="lib" path="jars/mail/mail.jar"/> <classpathentry kind="lib" path="jars/activation/activation.jar"/> <classpathentry kind="lib" path="jars/commons-email/commons-email-1.1.jar"/> + <classpathentry kind="lib" path="jars/commons-io/commons-io-1.4.jar"/> <classpathentry kind="output" path="bin"/> </classpath> Modified: trunk/Jmol-FAH/build.xml =================================================================== --- trunk/Jmol-FAH/build.xml 2008-11-08 17:00:07 UTC (rev 10266) +++ trunk/Jmol-FAH/build.xml 2008-11-08 17:21:46 UTC (rev 10267) @@ -19,6 +19,9 @@ <property name="commons-email.dir" value="jars/commons-email" /> <property name="commons-email.jar" value="commons-email-1.1.jar" /> <property name="commons-email.lic" value="LICENSE_commonsemail.txt" /> + <property name="commons-io.dir" value="jars/commons-io" /> + <property name="commons-io.jar" value="commons-io-1.4.jar" /> + <property name="commons-io.lic" value="LICENSE_commonsio.txt" /> <property name="mail.dir" value="jars/mail" /> <property name="mail.jar" value="mail.jar" /> <property name="mail.lic" value="LICENSE_mail.txt" /> @@ -61,6 +64,10 @@ <include name="${commons-email.jar}" /> <include name="${commons-email.lic}" /> </fileset> + <fileset dir="${commons-io.dir}"> + <include name="${commons-io.jar}" /> + <include name="${commons-io.lic}" /> + </fileset> </zip> </target> Added: trunk/Jmol-FAH/jars/commons-io/LICENSE_commonsio.txt =================================================================== --- trunk/Jmol-FAH/jars/commons-io/LICENSE_commonsio.txt (rev 0) +++ trunk/Jmol-FAH/jars/commons-io/LICENSE_commonsio.txt 2008-11-08 17:21:46 UTC (rev 10267) @@ -0,0 +1,203 @@ + + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. Definitions. + + "License" shall mean the terms and conditions for use, reproduction, + and distribution as defined by Sections 1 through 9 of this document. + + "Licensor" shall mean the copyright owner or entity authorized by + the copyright owner that is granting the License. + + "Legal Entity" shall mean the union of the acting entity and all + other entities that control, are controlled by, or are under common + control with that entity. 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Unless required by applicable law or + agreed to in writing, Licensor provides the Work (and each + Contributor provides its Contributions) on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or + implied, including, without limitation, any warranties or conditions + of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A + PARTICULAR PURPOSE. You are solely responsible for determining the + appropriateness of using or redistributing the Work and assume any + risks associated with Your exercise of permissions under this License. + + 8. Limitation of Liability. In no event and under no legal theory, + whether in tort (including negligence), contract, or otherwise, + unless required by applicable law (such as deliberate and grossly + negligent acts) or agreed to in writing, shall any Contributor be + liable to You for damages, including any direct, indirect, special, + incidental, or consequential damages of any character arising as a + result of this License or out of the use or inability to use the + Work (including but not limited to damages for loss of goodwill, + work stoppage, computer failure or malfunction, or any and all + other commercial damages or losses), even if such Contributor + has been advised of the possibility of such damages. + + 9. Accepting Warranty or Additional Liability. While redistributing + the Work or Derivative Works thereof, You may choose to offer, + and charge a fee for, acceptance of support, warranty, indemnity, + or other liability obligations and/or rights consistent with this + License. However, in accepting such obligations, You may act only + on Your own behalf and on Your sole responsibility, not on behalf + of any other Contributor, and only if You agree to indemnify, + defend, and hold each Contributor harmless for any liability + incurred by, or claims asserted against, such Contributor by reason + of your accepting any such warranty or additional liability. + + END OF TERMS AND CONDITIONS + + APPENDIX: How to apply the Apache License to your work. + + To apply the Apache License to your work, attach the following + boilerplate notice, with the fields enclosed by brackets "[]" + replaced with your own identifying information. (Don't include + the brackets!) The text should be enclosed in the appropriate + comment syntax for the file format. We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright [yyyy] [name of copyright owner] + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. + Property changes on: trunk/Jmol-FAH/jars/commons-io/LICENSE_commonsio.txt ___________________________________________________________________ Added: svn:mime-type + text/plain Added: trunk/Jmol-FAH/jars/commons-io/commons-io-1.4.jar =================================================================== (Binary files differ) Property changes on: trunk/Jmol-FAH/jars/commons-io/commons-io-1.4.jar ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Modified: trunk/Jmol-FAH/src/org/jmol/fah/Jmol-FAH.properties =================================================================== --- trunk/Jmol-FAH/src/org/jmol/fah/Jmol-FAH.properties 2008-11-08 17:00:07 UTC (rev 10266) +++ trunk/Jmol-FAH/src/org/jmol/fah/Jmol-FAH.properties 2008-11-08 17:21:46 UTC (rev 10267) @@ -3,4 +3,4 @@ # # Version # -Version=0.8 +Version=0.9 Modified: trunk/Jmol-FAH/src/org/jmol/fah/checkxyz/Check.java =================================================================== --- trunk/Jmol-FAH/src/org/jmol/fah/checkxyz/Check.java 2008-11-08 17:00:07 UTC (rev 10266) +++ trunk/Jmol-FAH/src/org/jmol/fah/checkxyz/Check.java 2008-11-08 17:21:46 UTC (rev 10267) @@ -27,17 +27,12 @@ import java.awt.event.ActionEvent; import java.awt.event.ActionListener; -import java.io.BufferedInputStream; -import java.io.BufferedOutputStream; import java.io.BufferedReader; import java.io.File; import java.io.FileFilter; import java.io.FileNotFoundException; -import java.io.FileOutputStream; import java.io.FileReader; import java.io.IOException; -import java.io.InputStream; -import java.io.OutputStream; import java.net.MalformedURLException; import java.net.URL; import java.text.DateFormat; @@ -47,6 +42,8 @@ import javax.swing.JOptionPane; +import org.apache.commons.io.FileUtils; + /** * Checking for missing XYZ files for http://www.jmol.org/fah * @@ -86,8 +83,9 @@ } }; File configDirectory = new File(new File(System.getProperty("user.home")), ".jmol"); - if (!configDirectory.mkdirs() && - (!configDirectory.exists() || !configDirectory.isDirectory())) { + try { + FileUtils.forceMkdir(configDirectory); + } catch (IOException e) { System.out.println("Error creating directory " + configDirectory.toString()); } availableProjects = new File(configDirectory, "availableProjects"); @@ -509,9 +507,7 @@ } } try { - if (configuration.getDetailedOutput()) { - System.out.print("Found new project :)"); - } + System.out.println("Found new project :) " + project); File[] files = new File[4]; files[0] = file; if ((topologyFile != null) && (trajectoryFile != null)) { @@ -521,8 +517,35 @@ files[3] = logFile; } } - MailSender sender = new MailSender(configuration, project, files, false); - sender.sendMail(); + if ((configuration.getMailServer() != null) && + (!"".equals(configuration.getMailServer())) && + (configuration.getUserMail() != null) && + (!"".equals(configuration.getUserMail())) && + (configuration.getUserName() != null) && + (!"".equals(configuration.getUserName()))) { + MailSender sender = new MailSender(configuration, project, files, false); + sender.sendMail(); + } + if ((configuration.getSaveDirectory() != null) && + (!"".equals(configuration.getSaveDirectory()))) { + File saveDir = new File(configuration.getSaveDirectory()); + try { + FileUtils.forceMkdir(saveDir); + } catch (IOException e) { + System.out.println("Error creating directory " + saveDir.getAbsolutePath()); + } + for (int i = 0; i < files.length; i++) { + File saveProjectDir = new File(saveDir, "p" + project); + if (files[i] != null) { + File destFile = new File(saveProjectDir, files[i].getName()); + try { + FileUtils.copyFile(files[i], destFile); + } catch (IOException e) { + System.out.println("Error saving file " + files[i]); + } + } + } + } if (!existingProjects.contains(project)) { if (!configuration.hasBeenSent(project)) { configuration.addSentFile(project); @@ -594,63 +617,27 @@ } /** - * Download a file locally. - * - * @param inputFile Input file. - * @param outputFile Output file. - * @return Flag indicating if the download was successful. + * Download the list of available files from http://www.jmol.org/ */ - private boolean downloadFile(String inputFile, File outputFile) { - OutputStream os = null; - InputStream is = null; + private void downloadAvailableFiles() { try { - os = new BufferedOutputStream(new FileOutputStream(outputFile, false)); - URL url = new URL(inputFile); - is = new BufferedInputStream(url.openStream()); - int read = -1; - while ((read = is.read()) != -1) { - os.write(read); - } - return true; + FileUtils.copyURLToFile( + new URL("http://www.jmol.org/fah/availableProjects.txt"), + availableProjects); } catch (MalformedURLException e) { - outputError("Downloading available files", e); + // } catch (IOException e) { - outputError("Downloading available files", e); - } finally { - if (os != null) { - try { - os.close(); - } catch (IOException e) { - outputError("Closing OutputStream", e); - } - } - if (is != null) { - try { - is.close(); - } catch (IOException e) { - outputError("Closing InputStream", e); - } - } + System.out.println("Error retrieving availableProjects.txt from Jmol website"); } - return false; - } - - /** - * Download the list of available files from http://www.jmol.org/ - */ - private void downloadAvailableFiles() { - if (!availableProjectsDownloaded) { - availableProjectsDownloaded = downloadFile("http://www.jmol.org/fah/availableProjects.txt", availableProjects); - if (availableProjectsDownloaded) { - existingProjects.clear(); - } + try { + FileUtils.copyURLToFile( + new URL("http://www.jmol.org/fah/availableAmber.txt"), + availableAmbers); + } catch (MalformedURLException e) { + // + } catch (IOException e) { + System.out.println("Error retrieving availableAmber.txt from Jmol website"); } - if (!availableAmbersDownloaded) { - availableAmbersDownloaded = downloadFile("http://www.jmol.org/fah/availableAmber.txt", availableAmbers); - if (availableAmbersDownloaded) { - existingAmbers.clear(); - } - } } /** Modified: trunk/Jmol-FAH/src/org/jmol/fah/checkxyz/Configuration.java =================================================================== --- trunk/Jmol-FAH/src/org/jmol/fah/checkxyz/Configuration.java 2008-11-08 17:00:07 UTC (rev 10266) +++ trunk/Jmol-FAH/src/org/jmol/fah/checkxyz/Configuration.java 2008-11-08 17:21:46 UTC (rev 10267) @@ -47,6 +47,7 @@ private String userMail; private String login; private String password; + private String saveDir; private boolean loop; private int basicInterval; private int threshold; @@ -69,6 +70,7 @@ userMail = ""; login = ""; password = ""; + saveDir = ""; loop = false; basicInterval = 30; threshold = 90; @@ -113,6 +115,7 @@ userMail = props.getProperty("userMail", userMail); login = props.getProperty("login", login); password = props.getProperty("password", password); + saveDir = props.getProperty("saveDir", saveDir); tmpBoolean = Boolean.valueOf(props.getProperty("loop", Boolean.toString(loop))); loop = (tmpBoolean != null) ? tmpBoolean.booleanValue() : false; tmpString = props.getProperty("basicInterval", Integer.toString(basicInterval)); @@ -176,6 +179,7 @@ props.setProperty("userMail", userMail); props.setProperty("login", login); props.setProperty("password", password); + props.setProperty("saveDir", saveDir); props.setProperty("loop", Boolean.toString(loop)); props.setProperty("basicInterval", Integer.toString(basicInterval)); props.setProperty("threshold", Integer.toString(threshold)); @@ -212,11 +216,17 @@ * @return Indicates if the configuration is done. */ public boolean isConfigured() { + boolean mailConfigured = true; + mailConfigured &= ((mailServer != null) && !mailServer.isEmpty()); + mailConfigured &= ((userMail != null) && !userMail.isEmpty()); + mailConfigured &= ((userName != null) && !userName.isEmpty()); + + boolean saveConfigured = true; + saveConfigured &= ((saveDir != null) && !saveDir.isEmpty()); + boolean configured = true; - configured &= ((userName != null) && !userName.equals("")); - configured &= ((mailServer != null) && !mailServer.equals("")); - configured &= ((userMail != null) && !userMail.equals("")); configured &= ((directories != null) && !directories.isEmpty()); + configured &= (mailConfigured || saveConfigured); return configured; } @@ -323,6 +333,20 @@ } /** + * @param dir Save directory. + */ + public void setSaveDirectory(String dir) { + if (dir != null) { + saveDir = dir.trim(); + } else { + saveDir = ""; + } + } + public String getSaveDirectory() { + return saveDir; + } + + /** * @param loop Loop. */ public void setLoop(boolean loop) { Modified: trunk/Jmol-FAH/src/org/jmol/fah/checkxyz/ConfigurationWindow.java =================================================================== --- trunk/Jmol-FAH/src/org/jmol/fah/checkxyz/ConfigurationWindow.java 2008-11-08 17:00:07 UTC (rev 10266) +++ trunk/Jmol-FAH/src/org/jmol/fah/checkxyz/ConfigurationWindow.java 2008-11-08 17:21:46 UTC (rev 10267) @@ -76,6 +76,7 @@ private JTextField textUserMail = null; private JTextField textUserLogin = null; private JTextField textUserPassword = null; + private JTextField textSaveDir = null; private JCheckBox chkLoop = null; private JFormattedTextField textBasicInterval = null; private JFormattedTextField textThreshold = null; @@ -344,6 +345,22 @@ constraints.gridy++; + // Save directory + JLabel labelSaveDir = new JLabel("Save directory :", SwingConstants.RIGHT); + constraints.gridx = 0; + constraints.weightx = 0; + constraints.anchor = GridBagConstraints.EAST; + panel.add(labelSaveDir, constraints); + + textSaveDir = new JTextField(configuration.getSaveDirectory(), 15); + textSaveDir.setToolTipText("The directory in which sent files are also copied locally."); + constraints.gridx++; + constraints.weightx = 1; + constraints.anchor = GridBagConstraints.WEST; + panel.add(textSaveDir, constraints); + + constraints.gridy++; + // Loop chkLoop = new JCheckBox("Loop", configuration.getLoop()); chkLoop.setToolTipText("Check this if you want the tool to check regularly for missing files"); @@ -576,6 +593,7 @@ configuration.setUserMail(textUserMail.getText()); configuration.setLogin(textUserLogin.getText()); configuration.setPassword(textUserPassword.getText()); + configuration.setSaveDirectory(textSaveDir.getText()); configuration.setLoop(chkLoop.isSelected()); tmpValue = textBasicInterval.getValue(); if (tmpValue instanceof Long) { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2008-11-09 11:43:54
|
Revision: 10274 http://jmol.svn.sourceforge.net/jmol/?rev=10274&view=rev Author: nicove Date: 2008-11-09 11:40:58 +0000 (Sun, 09 Nov 2008) Log Message: ----------- Folding@Home Modified Paths: -------------- trunk/Jmol-FAH/build.xml trunk/Jmol-FAH/src/org/jmol/fah/Jmol-FAH.properties Modified: trunk/Jmol-FAH/build.xml =================================================================== --- trunk/Jmol-FAH/build.xml 2008-11-09 08:30:12 UTC (rev 10273) +++ trunk/Jmol-FAH/build.xml 2008-11-09 11:40:58 UTC (rev 10274) @@ -36,7 +36,7 @@ </fileset> <manifest> <attribute name="Main-Class" value="org.jmol.fah.checkxyz.Check" /> - <attribute name="Class-Path" value="${activation.jar} ${mail.jar} ${commons-email.jar}" /> + <attribute name="Class-Path" value="${activation.jar} ${mail.jar} ${commons-email.jar} ${commons-io.jar}" /> </manifest> </jar> </target> Modified: trunk/Jmol-FAH/src/org/jmol/fah/Jmol-FAH.properties =================================================================== --- trunk/Jmol-FAH/src/org/jmol/fah/Jmol-FAH.properties 2008-11-09 08:30:12 UTC (rev 10273) +++ trunk/Jmol-FAH/src/org/jmol/fah/Jmol-FAH.properties 2008-11-09 11:40:58 UTC (rev 10274) @@ -3,4 +3,4 @@ # # Version # -Version=0.9 +Version=1.0 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2009-01-24 11:27:05
|
Revision: 10578 http://jmol.svn.sourceforge.net/jmol/?rev=10578&view=rev Author: nicove Date: 2009-01-24 11:27:00 +0000 (Sat, 24 Jan 2009) Log Message: ----------- Folding@Home Modified Paths: -------------- trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java Added Paths: ----------- trunk/Jmol-FAH/projects/p2464.xyz.gz trunk/Jmol-FAH/projects/p2498.xyz.gz trunk/Jmol-FAH/projects/p2499.xyz.gz trunk/Jmol-FAH/projects/p4447.xyz.gz trunk/Jmol-FAH/projects/p4454.xyz.gz trunk/Jmol-FAH/projects/p4458.xyz.gz trunk/Jmol-FAH/projects/p4463.xyz.gz Added: trunk/Jmol-FAH/projects/p2464.xyz.gz =================================================================== (Binary files differ) Property changes on: trunk/Jmol-FAH/projects/p2464.xyz.gz ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: trunk/Jmol-FAH/projects/p2498.xyz.gz =================================================================== (Binary files differ) Property changes on: trunk/Jmol-FAH/projects/p2498.xyz.gz ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: trunk/Jmol-FAH/projects/p2499.xyz.gz =================================================================== (Binary files differ) Property changes on: trunk/Jmol-FAH/projects/p2499.xyz.gz ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: trunk/Jmol-FAH/projects/p4447.xyz.gz =================================================================== (Binary files differ) Property changes on: trunk/Jmol-FAH/projects/p4447.xyz.gz ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: trunk/Jmol-FAH/projects/p4454.xyz.gz =================================================================== (Binary files differ) Property changes on: trunk/Jmol-FAH/projects/p4454.xyz.gz ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: trunk/Jmol-FAH/projects/p4458.xyz.gz =================================================================== (Binary files differ) Property changes on: trunk/Jmol-FAH/projects/p4458.xyz.gz ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: trunk/Jmol-FAH/projects/p4463.xyz.gz =================================================================== (Binary files differ) Property changes on: trunk/Jmol-FAH/projects/p4463.xyz.gz ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Modified: trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java =================================================================== --- trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java 2009-01-24 11:04:21 UTC (rev 10577) +++ trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java 2009-01-24 11:27:00 UTC (rev 10578) @@ -740,6 +740,8 @@ info._fciCore = CoreType.NVIDIA_DEV; } else if ("QMD".equalsIgnoreCase(core)) { info._fciCore = CoreType.QMD; + } else if ("SHARPEN".equalsIgnoreCase(core)) { + info._fciCore = CoreType.SHARPEN; } else if ("TINKER".equalsIgnoreCase(core)) { info._fciCore = CoreType.TINKER; } else { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2009-03-03 15:15:58
|
Revision: 10695 http://jmol.svn.sourceforge.net/jmol/?rev=10695&view=rev Author: nicove Date: 2009-03-03 15:15:47 +0000 (Tue, 03 Mar 2009) Log Message: ----------- Folding@Home Modified Paths: -------------- trunk/Jmol-FAH/src/org/jmol/fah/CoreType.java trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java Added Paths: ----------- trunk/Jmol-FAH/projects/p3861.xyz.gz trunk/Jmol-FAH/projects/p3862.xyz.gz Added: trunk/Jmol-FAH/projects/p3861.xyz.gz =================================================================== (Binary files differ) Property changes on: trunk/Jmol-FAH/projects/p3861.xyz.gz ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: trunk/Jmol-FAH/projects/p3862.xyz.gz =================================================================== (Binary files differ) Property changes on: trunk/Jmol-FAH/projects/p3862.xyz.gz ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Modified: trunk/Jmol-FAH/src/org/jmol/fah/CoreType.java =================================================================== --- trunk/Jmol-FAH/src/org/jmol/fah/CoreType.java 2009-03-03 14:59:53 UTC (rev 10694) +++ trunk/Jmol-FAH/src/org/jmol/fah/CoreType.java 2009-03-03 15:15:47 UTC (rev 10695) @@ -71,6 +71,9 @@ if (code.equalsIgnoreCase(GROGPU2._code)) { return GROGPU2; } + if (code.equalsIgnoreCase(GROGPU2_MT._code)) { + return GROGPU2_MT; + } if (code.equalsIgnoreCase(GROMACS._code)) { return GROMACS; } @@ -143,6 +146,9 @@ if (name.equalsIgnoreCase(GROGPU2._name)) { return GROGPU2; } + if (name.equalsIgnoreCase(GROGPU2_MT._name)) { + return GROGPU2_MT; + } if (name.equalsIgnoreCase(GROMACS._name)) { return GROMACS; } @@ -208,6 +214,7 @@ static public final CoreType GROCVS = new CoreType("GroCVS", "GC", true); //$NON-NLS-1$ //$NON-NLS-2$ static public final CoreType GROGPU = new CoreType("GroGPU", "GG", false); //$NON-NLS-1$ //$NON-NLS-2$ static public final CoreType GROGPU2 = new CoreType("GroGPU2", "GG2", false); //$NON-NLS-1$ //$NON-NLS-2$ + static public final CoreType GROGPU2_MT = new CoreType("GroGPU2-MT", "GG2MT", false); //$NON-NLS-1$ //$NON-NLS-2$ static public final CoreType GROMACS = new CoreType("Gromacs", "G", true); //$NON-NLS-1$ //$NON-NLS-2$ static public final CoreType GROMACS_PS3 = new CoreType("Gro-PS3", "G3", false); //$NON-NLS-1$ //$NON-NLS-2$ static public final CoreType GROMACS_SIMT = new CoreType("GroSimT", "GST", true); //$NON-NLS-1$ //$NON-NLS-2$ Modified: trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java =================================================================== --- trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java 2009-03-03 14:59:53 UTC (rev 10694) +++ trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java 2009-03-03 15:15:47 UTC (rev 10695) @@ -722,6 +722,8 @@ info._fciCore = CoreType.GROGPU; } else if ("GROGPU2".equalsIgnoreCase(core)) { info._fciCore = CoreType.GROGPU2; + } else if ("GROGPU2-MT".equalsIgnoreCase(core)) { + info._fciCore = CoreType.GROGPU2_MT; } else if ("GROMACS".equalsIgnoreCase(core)) { info._fciCore = CoreType.GROMACS; } else if ("GROMACS33".equalsIgnoreCase(core)) { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2009-03-07 18:38:22
|
Revision: 10707 http://jmol.svn.sourceforge.net/jmol/?rev=10707&view=rev Author: nicove Date: 2009-03-07 18:38:18 +0000 (Sat, 07 Mar 2009) Log Message: ----------- Folding@Home Modified Paths: -------------- trunk/Jmol-FAH/src/org/jmol/fah/CoreType.java Added Paths: ----------- trunk/Jmol-FAH/projects/p2497.xyz.gz Added: trunk/Jmol-FAH/projects/p2497.xyz.gz =================================================================== (Binary files differ) Property changes on: trunk/Jmol-FAH/projects/p2497.xyz.gz ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Modified: trunk/Jmol-FAH/src/org/jmol/fah/CoreType.java =================================================================== --- trunk/Jmol-FAH/src/org/jmol/fah/CoreType.java 2009-03-07 17:44:53 UTC (rev 10706) +++ trunk/Jmol-FAH/src/org/jmol/fah/CoreType.java 2009-03-07 18:38:18 UTC (rev 10707) @@ -204,7 +204,7 @@ // Cores static public final CoreType UNKNOWN = new CoreType(null, null, true); static public final CoreType A0GROMACS = new CoreType("Gromacs33", "A0", true); //$NON-NLS-1$ //$NON-NLS-2$ - static public final CoreType A4GROMACS = new CoreType("GRO-A4", "A4", true); //$NON-NLS-1$ //$NON-NLS-2$ + static public final CoreType A4GROMACS = new CoreType("GRO-A4", "A4", false); //$NON-NLS-1$ //$NON-NLS-2$ static public final CoreType AMBER = new CoreType("Amber", "A", true); //$NON-NLS-1$ //$NON-NLS-2$ static public final CoreType ATI_DEV = new CoreType("ATI-DEV", "AD", false); //$NON-NLS-1$ //$NON-NLS-2$ static public final CoreType DGROMACS = new CoreType("DGromacs", "DG", true); //$NON-NLS-1$ //$NON-NLS-2$ This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2009-11-03 19:04:52
|
Revision: 11660 http://jmol.svn.sourceforge.net/jmol/?rev=11660&view=rev Author: nicove Date: 2009-11-03 19:04:45 +0000 (Tue, 03 Nov 2009) Log Message: ----------- Folding@Home Modified Paths: -------------- trunk/Jmol-FAH/src/org/jmol/fah/CoreType.java trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java Added Paths: ----------- trunk/Jmol-FAH/projects/p6313.xyz.gz trunk/Jmol-FAH/projects/p6317.xyz.gz Added: trunk/Jmol-FAH/projects/p6313.xyz.gz =================================================================== (Binary files differ) Property changes on: trunk/Jmol-FAH/projects/p6313.xyz.gz ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: trunk/Jmol-FAH/projects/p6317.xyz.gz =================================================================== (Binary files differ) Property changes on: trunk/Jmol-FAH/projects/p6317.xyz.gz ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Modified: trunk/Jmol-FAH/src/org/jmol/fah/CoreType.java =================================================================== --- trunk/Jmol-FAH/src/org/jmol/fah/CoreType.java 2009-11-03 03:43:02 UTC (rev 11659) +++ trunk/Jmol-FAH/src/org/jmol/fah/CoreType.java 2009-11-03 19:04:45 UTC (rev 11660) @@ -41,6 +41,9 @@ if (code.equalsIgnoreCase(A0GROMACS._code)) { return A0GROMACS; } + if (code.equalsIgnoreCase(A3GROMACS._code)) { + return A3GROMACS; + } if (code.equalsIgnoreCase(A4GROMACS._code)) { return A4GROMACS; } @@ -116,6 +119,9 @@ if (name.equalsIgnoreCase(A0GROMACS._name)) { return A0GROMACS; } + if (name.equalsIgnoreCase(A3GROMACS._name)) { + return A3GROMACS; + } if (name.equalsIgnoreCase(A4GROMACS._name)) { return A4GROMACS; } @@ -204,6 +210,7 @@ // Cores static public final CoreType UNKNOWN = new CoreType(null, null, true); static public final CoreType A0GROMACS = new CoreType("Gromacs33", "A0", true); //$NON-NLS-1$ //$NON-NLS-2$ + static public final CoreType A3GROMACS = new CoreType("GRO-A3", "A3", false); //$NON-NLS-1$ //$NON-NLS-2$ static public final CoreType A4GROMACS = new CoreType("GRO-A4", "A4", false); //$NON-NLS-1$ //$NON-NLS-2$ static public final CoreType AMBER = new CoreType("Amber", "A", true); //$NON-NLS-1$ //$NON-NLS-2$ static public final CoreType ATI_DEV = new CoreType("ATI-DEV", "AD", false); //$NON-NLS-1$ //$NON-NLS-2$ Modified: trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java =================================================================== --- trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java 2009-11-03 03:43:02 UTC (rev 11659) +++ trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java 2009-11-03 19:04:45 UTC (rev 11660) @@ -730,6 +730,8 @@ info._fciCore = CoreType.A0GROMACS; } else if ("GROMACS-SMP".equalsIgnoreCase(core)) { info._fciCore = CoreType.GROMACS_SMP; + } else if ("GRO-A3".equalsIgnoreCase(core)) { + info._fciCore = CoreType.A3GROMACS; } else if ("GRO-A4".equalsIgnoreCase(core)) { info._fciCore = CoreType.A4GROMACS; } else if ("GRO-PS3".equalsIgnoreCase(core)) { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2009-11-06 20:18:33
|
Revision: 11690 http://jmol.svn.sourceforge.net/jmol/?rev=11690&view=rev Author: nicove Date: 2009-11-06 20:18:18 +0000 (Fri, 06 Nov 2009) Log Message: ----------- Folding@Home Modified Paths: -------------- trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java Added Paths: ----------- trunk/Jmol-FAH/projects/p10001.xyz.gz Added: trunk/Jmol-FAH/projects/p10001.xyz.gz =================================================================== (Binary files differ) Property changes on: trunk/Jmol-FAH/projects/p10001.xyz.gz ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Modified: trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java =================================================================== --- trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java 2009-11-06 19:41:23 UTC (rev 11689) +++ trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java 2009-11-06 20:18:18 UTC (rev 11690) @@ -138,7 +138,7 @@ */ Information createInfo(int projectNum) { Information info = new Information(); - if (projectNum < 9999) { // To avoid test projects + if (projectNum != 9999) { // To avoid test projects if (this._projectInfo.size() <= projectNum) { this._projectInfo.setSize(projectNum + 1); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2010-01-27 18:15:19
|
Revision: 12245 http://jmol.svn.sourceforge.net/jmol/?rev=12245&view=rev Author: nicove Date: 2010-01-27 18:15:06 +0000 (Wed, 27 Jan 2010) Log Message: ----------- Modified Paths: -------------- trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java Added Paths: ----------- trunk/Jmol-FAH/projects/p6020.xyz.gz trunk/Jmol-FAH/projects/p6021.xyz.gz Added: trunk/Jmol-FAH/projects/p6020.xyz.gz =================================================================== (Binary files differ) Property changes on: trunk/Jmol-FAH/projects/p6020.xyz.gz ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: trunk/Jmol-FAH/projects/p6021.xyz.gz =================================================================== (Binary files differ) Property changes on: trunk/Jmol-FAH/projects/p6021.xyz.gz ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Modified: trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java =================================================================== --- trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java 2010-01-27 17:00:54 UTC (rev 12244) +++ trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java 2010-01-27 18:15:06 UTC (rev 12245) @@ -1456,7 +1456,8 @@ if ((info._psContact == null) && (info._staticContact == null) && (info._fciContact != null) && - (!info._fciContact.equals("NA"))) { //$NON-NLS-1$ + (!info._fciContact.equals("NA")) && //$NON-NLS-1$ + (!info._fciContact.equals("n/a"))) { //$NON-NLS-1$ different = true; } if ((info._psCore == null) && @@ -1926,7 +1927,8 @@ } } else if (info._staticContact == null) { if ((info._fciContact != null) && - (!info._fciContact.equals("NA"))) { //$NON-NLS-1$ + (!info._fciContact.equals("NA")) && //$NON-NLS-1$ + (!info._fciContact.equals("n/a"))) { //$NON-NLS-1$ contactDifferent = true; } } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2011-03-01 18:19:39
|
Revision: 15238 http://jmol.svn.sourceforge.net/jmol/?rev=15238&view=rev Author: nicove Date: 2011-03-01 18:19:32 +0000 (Tue, 01 Mar 2011) Log Message: ----------- Folding@Home Modified Paths: -------------- trunk/Jmol-FAH/src/org/jmol/fah/CoreType.java trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java Added Paths: ----------- trunk/Jmol-FAH/projects/p10116.xyz.gz Added: trunk/Jmol-FAH/projects/p10116.xyz.gz =================================================================== (Binary files differ) Property changes on: trunk/Jmol-FAH/projects/p10116.xyz.gz ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Modified: trunk/Jmol-FAH/src/org/jmol/fah/CoreType.java =================================================================== --- trunk/Jmol-FAH/src/org/jmol/fah/CoreType.java 2011-02-26 19:11:16 UTC (rev 15237) +++ trunk/Jmol-FAH/src/org/jmol/fah/CoreType.java 2011-03-01 18:19:32 UTC (rev 15238) @@ -119,6 +119,9 @@ if (code.equalsIgnoreCase(TINKER._code)) { return TINKER; } + if (code.equalsIgnoreCase(UNLISTED._code)) { + return UNLISTED; + } } return UNKNOWN; } @@ -212,6 +215,9 @@ if (name.equalsIgnoreCase(TINKER._name)) { return TINKER; } + if (name.equalsIgnoreCase(UNLISTED._name)) { + return UNLISTED; + } } return UNKNOWN; } @@ -266,6 +272,7 @@ static public final CoreType QMD = new CoreType("QMD", "Q", true); //$NON-NLS-1$ //$NON-NLS-2$ static public final CoreType SHARPEN = new CoreType("Sharpen", "SP", true); //$NON-NLS-1$//$NON-NLS-2$ static public final CoreType TINKER = new CoreType("Tinker", "T", true); //$NON-NLS-1$//$NON-NLS-2$ + static public final CoreType UNLISTED = new CoreType("Unlisted", "UL", true); //$NON-NLS-1$//$NON-NLS-2$ // Attributes private final String _name; Modified: trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java =================================================================== --- trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java 2011-02-26 19:11:16 UTC (rev 15237) +++ trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java 2011-03-01 18:19:32 UTC (rev 15238) @@ -761,6 +761,8 @@ info._fciCore = CoreType.SHARPEN; } else if ("TINKER".equalsIgnoreCase(core)) { info._fciCore = CoreType.TINKER; + } else if ("UNLISTED".equalsIgnoreCase(core)) { + info._fciCore = CoreType.UNLISTED; } else { outputTextLn("FCI Core unknown: " + core); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2011-06-03 11:48:59
|
Revision: 15522 http://jmol.svn.sourceforge.net/jmol/?rev=15522&view=rev Author: nicove Date: 2011-06-03 11:48:52 +0000 (Fri, 03 Jun 2011) Log Message: ----------- Folding@Home Modified Paths: -------------- trunk/Jmol-FAH/src/org/jmol/fah/CoreType.java trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java Added Paths: ----------- trunk/Jmol-FAH/projects/p10081.xyz.gz Added: trunk/Jmol-FAH/projects/p10081.xyz.gz =================================================================== (Binary files differ) Property changes on: trunk/Jmol-FAH/projects/p10081.xyz.gz ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Modified: trunk/Jmol-FAH/src/org/jmol/fah/CoreType.java =================================================================== --- trunk/Jmol-FAH/src/org/jmol/fah/CoreType.java 2011-06-01 20:16:10 UTC (rev 15521) +++ trunk/Jmol-FAH/src/org/jmol/fah/CoreType.java 2011-06-03 11:48:52 UTC (rev 15522) @@ -50,6 +50,9 @@ if (code.equalsIgnoreCase(A5GROMACS._code)) { return A5GROMACS; } + if (code.equalsIgnoreCase(A6GROMACS._code)) { + return A6GROMACS; + } if (code.equalsIgnoreCase(AMBER._code)) { return AMBER; } @@ -146,6 +149,9 @@ if (name.equalsIgnoreCase(A5GROMACS._name)) { return A5GROMACS; } + if (name.equalsIgnoreCase(A6GROMACS._name)) { + return A6GROMACS; + } if (name.equalsIgnoreCase(AMBER._name)) { return AMBER; } @@ -249,6 +255,7 @@ static public final CoreType A3GROMACS = new CoreType("GRO-A3", "A3", false); //$NON-NLS-1$ //$NON-NLS-2$ static public final CoreType A4GROMACS = new CoreType("GRO-A4", "A4", false); //$NON-NLS-1$ //$NON-NLS-2$ static public final CoreType A5GROMACS = new CoreType("GRO-A5", "A5", false); //$NON-NLS-1$ //$NON-NLS-2$ + static public final CoreType A6GROMACS = new CoreType("GRO-A6", "A6", false); //$NON-NLS-1$ //$NON-NLS-2$ static public final CoreType AMBER = new CoreType("Amber", "A", true); //$NON-NLS-1$ //$NON-NLS-2$ static public final CoreType ATI_DEV = new CoreType("ATI-DEV", "AD", false); //$NON-NLS-1$ //$NON-NLS-2$ static public final CoreType DGROMACS = new CoreType("DGromacs", "DG", true); //$NON-NLS-1$ //$NON-NLS-2$ Modified: trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java =================================================================== --- trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java 2011-06-01 20:16:10 UTC (rev 15521) +++ trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java 2011-06-03 11:48:52 UTC (rev 15522) @@ -737,6 +737,8 @@ info._fciCore = CoreType.A4GROMACS; } else if ("GRO-A5".equalsIgnoreCase(core)) { info._fciCore = CoreType.A5GROMACS; + } else if ("GRO-A6".equalsIgnoreCase(core)) { + info._fciCore = CoreType.A6GROMACS; } else if ("GRO-PS3".equalsIgnoreCase(core)) { info._fciCore = CoreType.GROMACS_PS3; } else if ("GRO-SMP".equalsIgnoreCase(core)) { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2013-03-31 05:29:22
|
Revision: 18025 http://sourceforge.net/p/jmol/code/18025 Author: nicove Date: 2013-03-31 05:29:19 +0000 (Sun, 31 Mar 2013) Log Message: ----------- Folding@Home Modified Paths: -------------- trunk/Jmol-FAH/src/org/jmol/fah/CoreType.java trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java Added Paths: ----------- trunk/Jmol-FAH/projects/p6871.xyz.gz trunk/Jmol-FAH/projects/p6896.xyz.gz trunk/Jmol-FAH/projects/p6897.xyz.gz Added: trunk/Jmol-FAH/projects/p6871.xyz.gz =================================================================== (Binary files differ) Index: trunk/Jmol-FAH/projects/p6871.xyz.gz =================================================================== --- trunk/Jmol-FAH/projects/p6871.xyz.gz 2013-03-31 04:33:51 UTC (rev 18024) +++ trunk/Jmol-FAH/projects/p6871.xyz.gz 2013-03-31 05:29:19 UTC (rev 18025) Property changes on: trunk/Jmol-FAH/projects/p6871.xyz.gz ___________________________________________________________________ Added: svn:mime-type ## -0,0 +1 ## +application/octet-stream \ No newline at end of property Added: trunk/Jmol-FAH/projects/p6896.xyz.gz =================================================================== (Binary files differ) Index: trunk/Jmol-FAH/projects/p6896.xyz.gz =================================================================== --- trunk/Jmol-FAH/projects/p6896.xyz.gz 2013-03-31 04:33:51 UTC (rev 18024) +++ trunk/Jmol-FAH/projects/p6896.xyz.gz 2013-03-31 05:29:19 UTC (rev 18025) Property changes on: trunk/Jmol-FAH/projects/p6896.xyz.gz ___________________________________________________________________ Added: svn:mime-type ## -0,0 +1 ## +application/octet-stream \ No newline at end of property Added: trunk/Jmol-FAH/projects/p6897.xyz.gz =================================================================== (Binary files differ) Index: trunk/Jmol-FAH/projects/p6897.xyz.gz =================================================================== --- trunk/Jmol-FAH/projects/p6897.xyz.gz 2013-03-31 04:33:51 UTC (rev 18024) +++ trunk/Jmol-FAH/projects/p6897.xyz.gz 2013-03-31 05:29:19 UTC (rev 18025) Property changes on: trunk/Jmol-FAH/projects/p6897.xyz.gz ___________________________________________________________________ Added: svn:mime-type ## -0,0 +1 ## +application/octet-stream \ No newline at end of property Modified: trunk/Jmol-FAH/src/org/jmol/fah/CoreType.java =================================================================== --- trunk/Jmol-FAH/src/org/jmol/fah/CoreType.java 2013-03-31 04:33:51 UTC (rev 18024) +++ trunk/Jmol-FAH/src/org/jmol/fah/CoreType.java 2013-03-31 05:29:19 UTC (rev 18025) @@ -26,7 +26,7 @@ package org.jmol.fah; /** - * Typesafe enum class for core types + * Type safe enum class for core types */ public class CoreType { @@ -140,13 +140,16 @@ if (name.equalsIgnoreCase(A0GROMACS._name)) { return A0GROMACS; } - if (name.equalsIgnoreCase(A3GROMACS._name)) { + if (name.equalsIgnoreCase(A3GROMACS._name) || + name.equalsIgnoreCase(A3GROMACS._name2)) { return A3GROMACS; } - if (name.equalsIgnoreCase(A4GROMACS._name)) { + if (name.equalsIgnoreCase(A4GROMACS._name) || + name.equalsIgnoreCase(A4GROMACS._name2)) { return A4GROMACS; } - if (name.equalsIgnoreCase(A5GROMACS._name)) { + if (name.equalsIgnoreCase(A5GROMACS._name) || + name.equalsIgnoreCase(A5GROMACS._name2)) { return A5GROMACS; } if (name.equalsIgnoreCase(A6GROMACS._name)) { @@ -252,9 +255,9 @@ // Cores static public final CoreType UNKNOWN = new CoreType(null, null, true); static public final CoreType A0GROMACS = new CoreType("Gromacs33", "A0", true); //$NON-NLS-1$ //$NON-NLS-2$ - static public final CoreType A3GROMACS = new CoreType("GRO-A3", "A3", false); //$NON-NLS-1$ //$NON-NLS-2$ - static public final CoreType A4GROMACS = new CoreType("GRO-A4", "A4", false); //$NON-NLS-1$ //$NON-NLS-2$ - static public final CoreType A5GROMACS = new CoreType("GRO-A5", "A5", false); //$NON-NLS-1$ //$NON-NLS-2$ + static public final CoreType A3GROMACS = new CoreType("GRO-A3", "GRO_A3", "A3", false); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$ + static public final CoreType A4GROMACS = new CoreType("GRO-A4", "GRO_A4", "A4", false); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$ + static public final CoreType A5GROMACS = new CoreType("GRO-A5", "GRO_A5", "A5", false); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$ static public final CoreType A6GROMACS = new CoreType("GRO-A6", "A6", false); //$NON-NLS-1$ //$NON-NLS-2$ static public final CoreType AMBER = new CoreType("Amber", "A", true); //$NON-NLS-1$ //$NON-NLS-2$ static public final CoreType ATI_DEV = new CoreType("ATI-DEV", "AD", false); //$NON-NLS-1$ //$NON-NLS-2$ @@ -274,7 +277,7 @@ static public final CoreType NVIDIA_DEV = new CoreType("NVIDIA-DEV", "ND", false); //$NON-NLS-1$ //$NON-NLS-2$ static public final CoreType OPEN_MM_CL = new CoreType("OpenMM_OpenCL", "OC", true); //$NON-NLS-1$ //$NON-NLS-2$ static public final CoreType OPEN_MM_FERMI= new CoreType("OpenMMFermi", "OF", true); //$NON-NLS-1$ //$NON-NLS-2$ - static public final CoreType OPEN_MM_GPU = new CoreType("OpenMMGPU", "OG", true); //$NON-NLS-1$ //$NON-NLS-2$ + static public final CoreType OPEN_MM_GPU = new CoreType("OpenMMGPU", "GPU", "OG", true); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$ static public final CoreType PROTO_MOL = new CoreType("ProtoMol", "PM", true); //$NON-NLS-1$ //$NON-NLS-2$ static public final CoreType QMD = new CoreType("QMD", "Q", true); //$NON-NLS-1$ //$NON-NLS-2$ static public final CoreType SHARPEN = new CoreType("Sharpen", "SP", true); //$NON-NLS-1$//$NON-NLS-2$ @@ -283,6 +286,7 @@ // Attributes private final String _name; + private final String _name2; private final String _code; private final boolean _hasFile; @@ -294,7 +298,20 @@ * @param hasFile Flag indicating the present of a current.xyz file */ private CoreType(String name, String code, boolean hasFile) { + this(name, null, code, hasFile); + } + + /** + * Constructor for CoreType + * + * @param name Name of core + * @param name2 Second name of core + * @param code Letter code of core + * @param hasFile Flag indicating the present of a current.xyz file + */ + private CoreType(String name, String name2, String code, boolean hasFile) { this._name = name; + this._name2 = name2; this._code = code; this._hasFile = hasFile; } Modified: trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java =================================================================== --- trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java 2013-03-31 04:33:51 UTC (rev 18024) +++ trunk/Jmol-FAH/src/org/jmol/fah/ProjectInformation.java 2013-03-31 05:29:19 UTC (rev 18025) @@ -731,11 +731,14 @@ info._fciCore = CoreType.A0GROMACS; } else if ("GROMACS-SMP".equalsIgnoreCase(core)) { info._fciCore = CoreType.GROMACS_SMP; - } else if ("GRO-A3".equalsIgnoreCase(core)) { + } else if ("GRO-A3".equalsIgnoreCase(core) || + "GRO_A3".equalsIgnoreCase(core)) { info._fciCore = CoreType.A3GROMACS; - } else if ("GRO-A4".equalsIgnoreCase(core)) { + } else if ("GRO-A4".equalsIgnoreCase(core) || + "GRO_A4".equalsIgnoreCase(core)) { info._fciCore = CoreType.A4GROMACS; - } else if ("GRO-A5".equalsIgnoreCase(core)) { + } else if ("GRO-A5".equalsIgnoreCase(core) || + "GRO_A5".equalsIgnoreCase(core)) { info._fciCore = CoreType.A5GROMACS; } else if ("GRO-A6".equalsIgnoreCase(core)) { info._fciCore = CoreType.A6GROMACS; @@ -751,7 +754,8 @@ info._fciCore = CoreType.NVIDIA_DEV; } else if ("OPENMMFERMI".equalsIgnoreCase(core)) { info._fciCore = CoreType.OPEN_MM_FERMI; - } else if ("OPENMMGPU".equalsIgnoreCase(core)) { + } else if ("OPENMMGPU".equalsIgnoreCase(core) || + "GPU".equalsIgnoreCase(core)) { info._fciCore = CoreType.OPEN_MM_GPU; } else if ("OPENMM_OPENCL".equalsIgnoreCase(core)) { info._fciCore = CoreType.OPEN_MM_CL; @@ -1679,9 +1683,6 @@ return; } - outputText("Differences for project "); //$NON-NLS-1$ - outputTextLn(Integer.toString(projectNumber)); - // Check for unknown project if ((info._staticAtoms == null) && (info._staticContact == null) && @@ -1775,6 +1776,9 @@ return; } + outputText("Differences for project "); //$NON-NLS-1$ + outputTextLn(Integer.toString(projectNumber)); + //Print names difference boolean nameDifferent = false; if (info._psName != null) { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |