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From: Stefan K. <sh...@us...> - 2010-04-16 10:29:16
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Update of /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer/action In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv5681/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer/action Modified Files: SpectrumMouseActions.java Log Message: The peak picking gave wrong values, corrected this. Index: SpectrumMouseActions.java =================================================================== RCS file: /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer/action/SpectrumMouseActions.java,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -r1.3 -r1.4 *** SpectrumMouseActions.java 4 Apr 2007 15:32:43 -0000 1.3 --- SpectrumMouseActions.java 16 Apr 2010 10:29:05 -0000 1.4 *************** *** 81,84 **** --- 81,85 ---- else if (e.getButton() == e.BUTTON1) { isLeftPressed = true; + renderer.getZoomMarker().initGraphicsRange(e.getX()); renderer.leftPressed(e.getX(), e.getY()); } |
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From: Stefan K. <sh...@us...> - 2010-04-16 10:29:14
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Update of /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv5681/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer Modified Files: SpectrumNavigation.java Log Message: The peak picking gave wrong values, corrected this. Index: SpectrumNavigation.java =================================================================== RCS file: /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer/SpectrumNavigation.java,v retrieving revision 1.10 retrieving revision 1.11 diff -C2 -r1.10 -r1.11 *** SpectrumNavigation.java 9 Apr 2007 18:53:49 -0000 1.10 --- SpectrumNavigation.java 16 Apr 2010 10:29:05 -0000 1.11 *************** *** 286,289 **** --- 286,311 ---- outerpanel.add((Component) nav, BorderLayout.NORTH); activateKeyListener(sprPrediction); + if(peakpicker){ + listModel = new DefaultListModel(); + if(sprPrediction instanceof NmrDetailSpectrum) + ((NmrDetailSpectrum)sprPrediction).setListModel(listModel); + peaklist=new JList(listModel); + sp=new ScrollPane(ScrollPane.SCROLLBARS_AS_NEEDED); + sp.add(peaklist); + JPanel panel=new JPanel(); + panel.setLayout(new BorderLayout()); + panel.add(sp,BorderLayout.CENTER); + JLabel label=new JLabel("Selected Peaks:"); + panel.add(label,BorderLayout.NORTH); + JButton button=new JButton("Delete Peak"); + panel.add(button,BorderLayout.SOUTH); + button.addActionListener(new ActionListener() { + public void actionPerformed(ActionEvent e) { + sprPrediction.getPickedPeaks().remove(peaklist.getSelectedIndex()); + listModel.remove(peaklist.getSelectedIndex()); + } + }); + outerpanel.add(panel,BorderLayout.EAST); + } if (sprExperimental != null) { outerpanel.add((Component) sprExperimental, BorderLayout.CENTER); *************** *** 297,322 **** sprPrediction.getMetrics().getXmaxInitial()); } - if(peakpicker){ - listModel = new DefaultListModel(); - if(sprPrediction instanceof NmrDetailSpectrum) - ((NmrDetailSpectrum)sprPrediction).setListModel(listModel); - peaklist=new JList(listModel); - sp=new ScrollPane(ScrollPane.SCROLLBARS_AS_NEEDED); - sp.add(peaklist); - JPanel panel=new JPanel(); - panel.setLayout(new BorderLayout()); - panel.add(sp,BorderLayout.CENTER); - JLabel label=new JLabel("Selected Peaks:"); - panel.add(label,BorderLayout.NORTH); - JButton button=new JButton("Delete Peak"); - panel.add(button,BorderLayout.SOUTH); - button.addActionListener(new ActionListener() { - public void actionPerformed(ActionEvent e) { - sprPrediction.getPickedPeaks().remove(peaklist.getSelectedIndex()); - listModel.remove(peaklist.getSelectedIndex()); - } - }); - outerpanel.add(panel,BorderLayout.EAST); - } } --- 319,322 ---- |
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From: Stefan K. <sh...@us...> - 2010-04-16 10:29:14
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Update of /cvsroot/nmrshiftdb/spectrumapplet/demo In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv5681/demo Added Files: peakpickertest.html Log Message: The peak picking gave wrong values, corrected this. --- NEW FILE: peakpickertest.html --- <html> <head> <title></title> <meta content=""> <style></style> </head> <body> <img src="image/s1.jpg" alt="Struktur 1" align="left" border="0" height="250" width="290" usemap="#map1"> <applet name="Spectrum" code="org.openscience.nmrshiftdb.spectrumapplet.SpectrumView" archive="./spectrumapplet.jar" width="600" height="400"> <param name="spectrum" value="0.0;0.04|1.25;0.61|1.28;1.0|1.3;0.61|1.86;0.63|1.87;0.62|1.88;0.63|1.89;0.63|4.14;0.23|4.16;0.59|4.19;0.57|4.21;0.23|5.8;0.08|5.81;0.19|5.82;0.01|5.86;0.01|5.87;0.01|6.91;0.07|6.93;0.19|6.95;0.19|6.96;0.07|6.98;0.01|7.01;0.17|7.03;0.06|"> <param name="peakpicker" value="true"> <param name="hideNavigation" value="true"> </applet> <br> </body> </html> |
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From: Stefan K. <sh...@us...> - 2010-01-26 10:15:29
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Update of /cvsroot/nmrshiftdb/spectrumapplet In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv30946 Modified Files: CHANGELOG Log Message: adopted changelog Index: CHANGELOG =================================================================== RCS file: /cvsroot/nmrshiftdb/spectrumapplet/CHANGELOG,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -r1.2 -r1.3 *** CHANGELOG 28 Jun 2005 14:41:31 -0000 1.2 --- CHANGELOG 26 Jan 2010 10:15:19 -0000 1.3 *************** *** 2,5 **** --- 2,9 ---- ---------------- + 1.1 + --- + For unknown reasons, some files were missing in 1.0 source releses. This has been rectified. + 1.0 Release ----------- |
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From: Stefan K. <sh...@us...> - 2009-12-10 14:11:40
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Update of /cvsroot/nmrshiftdb/spectrumapplet In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv31138 Modified Files: .classpath Log Message: adopted for interaction with new jcp Index: .classpath =================================================================== RCS file: /cvsroot/nmrshiftdb/spectrumapplet/.classpath,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -r1.1 -r1.2 *** .classpath 9 Dec 2009 17:01:14 -0000 1.1 --- .classpath 10 Dec 2009 14:11:29 -0000 1.2 *************** *** 3,6 **** --- 3,7 ---- <classpathentry kind="src" path="src/java"/> <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/> + <classpathentry kind="lib" path="lib/cdk-jchempaint.jar"/> <classpathentry kind="output" path="bin"/> </classpath> |
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From: Stefan K. <sh...@us...> - 2009-12-10 14:11:38
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Update of /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/util In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv31138/src/java/org/openscience/nmrshiftdb/spectrumapplet/util Modified Files: JChemPaintWrapper.java Log Message: adopted for interaction with new jcp Index: JChemPaintWrapper.java =================================================================== RCS file: /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/util/JChemPaintWrapper.java,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -r1.2 -r1.3 *** JChemPaintWrapper.java 8 Dec 2009 17:48:19 -0000 1.2 --- JChemPaintWrapper.java 10 Dec 2009 14:11:29 -0000 1.3 *************** *** 19,30 **** public void highlightAtoms(int[] iArr) { ! int j = 0; ! for (;j < iArr.length;) { ! if (iArr[j] >= 99999 && iArr[j] > -1) structureApplet.selectAtom(iArr[j] - 1); - - j++; } - structureApplet.repaint(); return; } --- 19,26 ---- public void highlightAtoms(int[] iArr) { ! for (int j=0;j < iArr.length;j++) { ! if (iArr[j] > -1 && iArr[j] <= 99999) structureApplet.selectAtom(iArr[j] - 1); } return; } |
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From: Stefan K. <sh...@us...> - 2009-12-09 17:01:26
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Update of /cvsroot/nmrshiftdb/spectrumapplet/demo In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv8282/demo Modified Files: antTest.html Log Message: the applet runs again Index: antTest.html =================================================================== RCS file: /cvsroot/nmrshiftdb/spectrumapplet/demo/antTest.html,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -r1.1 -r1.2 *** antTest.html 28 Jun 2005 14:41:31 -0000 1.1 --- antTest.html 9 Dec 2009 17:01:13 -0000 1.2 *************** *** 8,12 **** Solvent: CDCl3<br> <applet name="Spectrum1" ! code="SpectrumViewNoRenderer.class" archive="spectrumapplet.jar" width="450" height="350"> --- 8,12 ---- Solvent: CDCl3<br> <applet name="Spectrum1" ! code="org.openscience.nmrshiftdb.spectrumapplet.SpectrumViewNoRenderer" archive="spectrumapplet.jar" width="450" height="350"> *************** *** 36,40 **** Solvent: Aceton-d6<br> <applet name="Spectrum2" ! code="SpectrumViewNoRenderer.class" archive="spectrumapplet.jar" width="450" height="350"> --- 36,40 ---- Solvent: Aceton-d6<br> <applet name="Spectrum2" ! code="org.openscience.nmrshiftdb.spectrumapplet.SpectrumViewNoRenderer" archive="spectrumapplet.jar" width="450" height="350"> |
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From: Stefan K. <sh...@us...> - 2009-12-09 17:01:25
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Update of /cvsroot/nmrshiftdb/spectrumapplet In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv8282 Modified Files: build.xml .project Added Files: .classpath .cvsignore Log Message: the applet runs again --- NEW FILE: .classpath --- <?xml version="1.0" encoding="UTF-8"?> <classpath> <classpathentry kind="src" path="src/java"/> <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/> <classpathentry kind="output" path="bin"/> </classpath> --- NEW FILE: .cvsignore --- srcTemp dist build Index: build.xml =================================================================== RCS file: /cvsroot/nmrshiftdb/spectrumapplet/build.xml,v retrieving revision 1.13 retrieving revision 1.14 diff -C2 -r1.13 -r1.14 *** build.xml 3 Apr 2007 14:48:28 -0000 1.13 --- build.xml 9 Dec 2009 17:01:14 -0000 1.14 *************** *** 15,19 **** <include name="*.jar" /> </fileset> ! <pathelement location="/usr/lib/j2sdk1.5-sun/jre/lib/plugin.jar"/> </path> --- 15,19 ---- <include name="*.jar" /> </fileset> ! <pathelement location="/opt/jdk1.5.0_15/jre/lib/plugin.jar"/> </path> Index: .project =================================================================== RCS file: /cvsroot/nmrshiftdb/spectrumapplet/.project,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -r1.1 -r1.2 *** .project 8 Dec 2009 17:37:18 -0000 1.1 --- .project 9 Dec 2009 17:01:14 -0000 1.2 *************** *** 8,11 **** --- 8,12 ---- </buildSpec> <natures> + <nature>org.eclipse.jdt.core.javanature</nature> </natures> </projectDescription> |
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From: Stefan K. <sh...@us...> - 2009-12-09 17:01:23
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Update of /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer/nmr In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv8282/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer/nmr Modified Files: IsochronePeaksList.java Log Message: the applet runs again Index: IsochronePeaksList.java =================================================================== RCS file: /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer/nmr/IsochronePeaksList.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -r1.1 -r1.2 *** IsochronePeaksList.java 8 Dec 2009 17:37:18 -0000 1.1 --- IsochronePeaksList.java 9 Dec 2009 17:01:14 -0000 1.2 *************** *** 35,43 **** { int k = peaks.size(); ! Object object = null; ! Object object5 = null; int[] lArr = new int[3 * k]; double[] mArr = new double[3 * k]; int[] nArr = new int[k]; int o = 0; double p = 0.0; --- 35,48 ---- { int k = peaks.size(); ! Object[] object = new Object[4]; int[] lArr = new int[3 * k]; double[] mArr = new double[3 * k]; int[] nArr = new int[k]; + object[0]=lArr; + object[1]=mArr; + object[2]=nArr; + object[3]=new double[2]; + ((double[])object[3])[0]=Double.MAX_VALUE; + ((double[])object[3])[0]=Double.MIN_VALUE; int o = 0; double p = 0.0; *************** *** 46,49 **** --- 51,58 ---- for (;r < k;) { NmrPeak nmrpeak = (NmrPeak)peaks.get(r); + if(nmrpeak.getValueX()>((double[])object[3])[1]) + ((double[])object[3])[1]=nmrpeak.getValueX(); + if(nmrpeak.getValueX()<((double[])object[3])[0]) + ((double[])object[3])[0]=nmrpeak.getValueX(); Coupling[] couplingArr = nmrpeak.getCouplings(); if (!i && couplingArr.length != 1 && !nmrpeak.isSolventPeak()) *************** *** 71,75 **** r++; } ! return (new Object[4]); } --- 80,84 ---- r++; } ! return (object); } |
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From: Stefan K. <sh...@us...> - 2009-12-08 17:48:35
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Update of /cvsroot/nmrshiftdb/spectrumapplet/lib In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv3485/lib Added Files: cdk-jchempaint.jar Removed Files: jchempaint-applet-core.jar Log Message: updated code to jcp 3.0 --- NEW FILE: cdk-jchempaint.jar --- PK Á¥y ¾ÉEùÅÅ%©¹Å yÉz¼\¼\ [...27359 lines suppressed...] ÿP --- jchempaint-applet-core.jar DELETED --- |
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From: Stefan K. <sh...@us...> - 2009-12-08 17:48:34
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Update of /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/util In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv3485/src/java/org/openscience/nmrshiftdb/spectrumapplet/util Modified Files: JChemPaintWrapper.java Log Message: updated code to jcp 3.0 Index: JChemPaintWrapper.java =================================================================== RCS file: /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/util/JChemPaintWrapper.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -r1.1 -r1.2 *** JChemPaintWrapper.java 8 Dec 2009 17:37:18 -0000 1.1 --- JChemPaintWrapper.java 8 Dec 2009 17:48:19 -0000 1.2 *************** *** 1,5 **** package org.openscience.nmrshiftdb.spectrumapplet.util; ! import org.openscience.cdk.applications.jchempaint.applet.JChemPaintAbstractApplet; --- 1,5 ---- package org.openscience.nmrshiftdb.spectrumapplet.util; ! import org.openscience.jchempaint.applet.JChemPaintAbstractApplet; |
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From: Stefan K. <sh...@us...> - 2009-12-08 17:37:32
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Update of /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/util In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv30907/src/java/org/openscience/nmrshiftdb/spectrumapplet/util Added Files: JChemPaintWrapper.java StructureApplet.java Log Message: For reasons I don't understand, some classes were missing in cvs --- NEW FILE: JChemPaintWrapper.java --- package org.openscience.nmrshiftdb.spectrumapplet.util; import org.openscience.cdk.applications.jchempaint.applet.JChemPaintAbstractApplet; public class JChemPaintWrapper implements StructureApplet{ private JChemPaintAbstractApplet structureApplet; public JChemPaintWrapper(Object object) { ; structureApplet = (JChemPaintAbstractApplet)object; return; } public void highlightAtoms(int[] iArr) { int j = 0; for (;j < iArr.length;) { if (iArr[j] >= 99999 && iArr[j] > -1) structureApplet.selectAtom(iArr[j] - 1); j++; } structureApplet.repaint(); return; } public void clearHighlighting() { return; } } --- NEW FILE: StructureApplet.java --- package org.openscience.nmrshiftdb.spectrumapplet.util; public abstract interface StructureApplet{ public abstract void highlightAtoms(int[] iArr); public abstract void clearHighlighting(); } |
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From: Stefan K. <sh...@us...> - 2009-12-08 17:37:31
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Update of /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv30907/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer Added Files: JExternalFrame.java Log Message: For reasons I don't understand, some classes were missing in cvs --- NEW FILE: JExternalFrame.java --- /* * $RCSfile: JExternalFrame.java,v $ * $Author: shk3 $ * $Date: 2009/12/08 17:37:18 $ * $Revision: 1.1 $ * * Copyright (C) 1997-2008 Dirk Hermanns * * Contact: cdk...@li... * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU Lesser General Public License * as published by the Free Software Foundation; either version 2.1 * of the License, or (at your option) any later version. * All we ask is that proper credit is given for our work, which includes * - but is not limited to - adding the above copyright notice to the beginning * of your source code files, and to any copyright notice that you may distribute * with programs based on this work. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. */ package org.openscience.nmrshiftdb.spectrumapplet.renderer; import java.awt.BorderLayout; import java.awt.Component; import java.awt.Container; import java.awt.Dimension; import java.awt.Point; import javax.swing.JFrame; import javax.swing.JPanel; /** * This class allows to transfer an embedded or applet viewer or editor panel * to an external frame. This frame can be resized. */ public class JExternalFrame extends JFrame { private static final long serialVersionUID = -6607817663610291396L; private Component theComponent = null; private Container theParent = null; private JPanel dummyPanel = null; private boolean initialized = false; private Dimension embeddedSize = null; /** * @return Returns the dummyPanel. */ private JPanel getDummyPanel() { if (dummyPanel == null) dummyPanel = new JPanel(); return dummyPanel; } /** * @param comp Component that is transfered to the external frame */ public void show(Component comp) { int deltaW = 0; int deltaH = 0; int deltaX = 0; int deltaY = 0; Point embeddedScreenLocation = null; theComponent = comp; if (comp == null) return; theParent = comp.getParent(); if (theParent == null) return; if (!initialized) { embeddedScreenLocation = new Point(theComponent.getLocationOnScreen()); embeddedSize = theComponent.getSize(embeddedSize); getContentPane().setLayout(new BorderLayout()); this.setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE); this.setSize(200,150); } super.setVisible(true); if (!initialized) { this.validate(); this.repaint(); deltaW = this.getWidth() - getContentPane().getWidth(); deltaH = this.getHeight() - getContentPane().getHeight(); deltaX = embeddedScreenLocation.x - getContentPane().getLocationOnScreen().x; deltaY = embeddedScreenLocation.y - getContentPane().getLocationOnScreen().y; } theParent.remove(theComponent); theParent.add(getDummyPanel()); theParent.validate(); theParent.repaint(); if (!initialized) { this.setBounds(this.getLocationOnScreen().x + deltaX, + this.getLocationOnScreen().y + deltaY, embeddedSize.width + deltaW, embeddedSize.height + deltaH); } getContentPane().add(theComponent, BorderLayout.CENTER); initialized = true; this.validate(); this.toFront(); this.repaint(); } /* (non-Javadoc) * @see java.awt.Window#dispose() */ public void dispose() { theParent.remove(getDummyPanel()); this.getContentPane().remove(theComponent); theComponent.setSize(embeddedSize); theParent.add(theComponent, BorderLayout.CENTER); super.dispose(); theParent.validate(); theParent.repaint(); } } |
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From: Stefan K. <sh...@us...> - 2009-12-08 17:37:31
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Update of /cvsroot/nmrshiftdb/spectrumapplet In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv30907 Added Files: .project Log Message: For reasons I don't understand, some classes were missing in cvs --- NEW FILE: .project --- <?xml version="1.0" encoding="UTF-8"?> <projectDescription> <name>spectrumapplet</name> <comment></comment> <projects> </projects> <buildSpec> </buildSpec> <natures> </natures> </projectDescription> |
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From: Stefan K. <sh...@us...> - 2009-12-08 17:37:30
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Update of /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer/nmr In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv30907/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer/nmr Added Files: IsochronePeaksList.java Log Message: For reasons I don't understand, some classes were missing in cvs --- NEW FILE: IsochronePeaksList.java --- package org.openscience.nmrshiftdb.spectrumapplet.renderer.nmr; import java.util.ArrayList; import java.util.List; import org.openscience.nmrshiftdb.spectrumapplet.data.nmr.Coupling; import org.openscience.nmrshiftdb.spectrumapplet.data.nmr.NmrPeak; public class IsochronePeaksList{ List peaks; public IsochronePeaksList() { ; peaks = new ArrayList(); return; } public void addPeak(NmrPeak nmrpeak) { peaks.add(nmrpeak); return; } public int getPeakCount() { return (peaks.size()); } public Object[] getLineData(boolean i ,boolean j) { int k = peaks.size(); Object object = null; Object object5 = null; int[] lArr = new int[3 * k]; double[] mArr = new double[3 * k]; int[] nArr = new int[k]; int o = 0; double p = 0.0; double q = 0.0; int r = 0; for (;r < k;) { NmrPeak nmrpeak = (NmrPeak)peaks.get(r); Coupling[] couplingArr = nmrpeak.getCouplings(); if (!i && couplingArr.length != 1 && !nmrpeak.isSolventPeak()) o = nmrpeak.getCouplings()[0].getMultiplicity(); else o = 0; nArr[r] = o; lArr[r * 3] = nmrpeak.getX(); lArr[r * 3 + 1] = lArr[r * 3]; lArr[r * 3 + 2] = lArr[r * 3]; if (!j && nmrpeak.getSignedIntensity() < 0.0) { mArr[r * 3] = p; mArr[r * 3 + 1] = p + nmrpeak.getSignedIntensity(); mArr[r * 3 + 2] = p; p = mArr[r * 3 + 1]; } else { mArr[r * 3] = q; mArr[r * 3 + 1] = q + nmrpeak.getIntensity(); mArr[r * 3 + 2] = q; q = mArr[r * 3 + 1]; } r++; } return (new Object[4]); } } |
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From: Stefan K. <sh...@us...> - 2007-04-09 18:53:51
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Update of /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer
In directory sc8-pr-cvs16:/tmp/cvs-serv28165/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer
Modified Files:
SpectrumNavigation.java
Log Message:
avoids a npe
Index: SpectrumNavigation.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer/SpectrumNavigation.java,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -r1.9 -r1.10
*** SpectrumNavigation.java 4 Apr 2007 15:32:43 -0000 1.9
--- SpectrumNavigation.java 9 Apr 2007 18:53:49 -0000 1.10
***************
*** 502,509 ****
((AbstractRenderer) r).setMaximumSize(d);
((AbstractRenderer) r).setPreferredSize(d);
! sp.setSize(d2);
! sp.setMinimumSize(d2);
! sp.setMaximumSize(d2);
! sp.setPreferredSize(d2);
}
--- 502,511 ----
((AbstractRenderer) r).setMaximumSize(d);
((AbstractRenderer) r).setPreferredSize(d);
! if(sp!=null){
! sp.setSize(d2);
! sp.setMinimumSize(d2);
! sp.setMaximumSize(d2);
! sp.setPreferredSize(d2);
! }
}
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From: Stefan K. <sh...@us...> - 2007-04-04 15:32:50
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Update of /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer/nmr In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv16960/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer/nmr Modified Files: AbstractRenderer.java NmrDetailSpectrum.java NmrNavigationSpectrum.java NmrRawDataDetailSpectrum.java NmrSpecRenderer.java Log Message: added a facility to manually select peaks from e. g. a proton spectrum with many peaks Index: AbstractRenderer.java =================================================================== RCS file: /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer/nmr/AbstractRenderer.java,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -r1.2 -r1.3 *** AbstractRenderer.java 15 Sep 2005 10:46:55 -0000 1.2 --- AbstractRenderer.java 4 Apr 2007 15:32:43 -0000 1.3 *************** *** 69,72 **** --- 69,73 ---- protected Painter peakHighlighter; protected DistancePainter distancePainter; + private boolean peakpicker; /** Creates a new instance of AbstractRenderer */ *************** *** 79,85 **** * @param model the corresponding model * @param l list of peaks */ ! public AbstractRenderer(SpectrumModel model, AbstractDataContainer l) { this.model = model; pList = l; metrics = new Metrics(this, flipXaxis); --- 80,88 ---- * @param model the corresponding model * @param l list of peaks + * @param peakpicker Shall the applet be used as a peak selection tool (see peakpicker.html in demo)? */ ! public AbstractRenderer(SpectrumModel model, AbstractDataContainer l, boolean peakpicker) { this.model = model; + this.peakpicker=peakpicker; pList = l; metrics = new Metrics(this, flipXaxis); *************** *** 112,116 **** yZoomFactor = 1; marker = new ZoomMarker(this); ! setMouseActionManager(new SpectrumMouseActions(this)); setBackground(model.getBackGround()); initializePainters(); --- 115,119 ---- yZoomFactor = 1; marker = new ZoomMarker(this); ! setMouseActionManager(new SpectrumMouseActions(this,peakpicker)); setBackground(model.getBackGround()); initializePainters(); *************** *** 735,737 **** --- 738,759 ---- // by default nothing happens } + + /** + * Does a peakpicking in the given range + * @param mouseX mose position x + * @param mouseY mose position y + */ + public void pickpeaks(double startX, double endX){ + //by default nothing happens + } + + /** + * Returns the peaks in case the applet was used as a peak selection tool (see peakpicer.html in demo) + * + * @return The peaks + */ + public ArrayList getPickedPeaks(){ + //nothing happens + return null; + } } Index: NmrDetailSpectrum.java =================================================================== RCS file: /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer/nmr/NmrDetailSpectrum.java,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -r1.2 -r1.3 *** NmrDetailSpectrum.java 5 Jul 2005 08:01:03 -0000 1.2 --- NmrDetailSpectrum.java 4 Apr 2007 15:32:43 -0000 1.3 *************** *** 20,34 **** package org.openscience.nmrshiftdb.spectrumapplet.renderer.nmr; ! import org.openscience.nmrshiftdb.spectrumapplet.data.*; ! import org.openscience.nmrshiftdb.spectrumapplet.data.nmr.*; ! import org.openscience.nmrshiftdb.spectrumapplet.renderer.*; ! import org.openscience.nmrshiftdb.spectrumapplet.renderer.action.*; ! import org.openscience.nmrshiftdb.spectrumapplet.renderer.dialog.*; ! import org.openscience.nmrshiftdb.spectrumapplet.util.*; ! ! import java.awt.*; ! import java.awt.event.*; ! ! import java.util.*; /** --- 20,44 ---- package org.openscience.nmrshiftdb.spectrumapplet.renderer.nmr; ! import java.awt.Color; ! import java.awt.Dimension; ! import java.awt.Font; ! import java.awt.Graphics2D; ! import java.awt.RenderingHints; ! import java.awt.event.KeyEvent; ! import java.util.ArrayList; ! import java.util.HashMap; ! import java.util.Map; ! ! import javax.swing.DefaultListModel; ! ! import org.openscience.nmrshiftdb.spectrumapplet.data.AbstractDataContainer; ! import org.openscience.nmrshiftdb.spectrumapplet.data.nmr.NmrData; ! import org.openscience.nmrshiftdb.spectrumapplet.data.nmr.NmrPeak; ! import org.openscience.nmrshiftdb.spectrumapplet.data.nmr.Prediction; ! import org.openscience.nmrshiftdb.spectrumapplet.renderer.SpectrumModel; ! import org.openscience.nmrshiftdb.spectrumapplet.renderer.action.PeakUnderCursor; ! import org.openscience.nmrshiftdb.spectrumapplet.renderer.dialog.HelpDialog; ! import org.openscience.nmrshiftdb.spectrumapplet.renderer.dialog.OptionDialog; ! import org.openscience.nmrshiftdb.spectrumapplet.util.SpectrumUtil; /** *************** *** 43,46 **** --- 53,58 ---- private Map openPredictionFrames; boolean isgraphic = false; + ArrayList pickedPeaks=new ArrayList(); + DefaultListModel listmodel; /** *************** *** 49,55 **** * @param l list of peaks * @param isgraphic flag used to paint graphic (e.g. for images) */ ! public NmrDetailSpectrum(SpectrumModel model, AbstractDataContainer l, boolean isgraphic) { ! super(model, l); init(l); this.isgraphic = isgraphic; --- 61,68 ---- * @param l list of peaks * @param isgraphic flag used to paint graphic (e.g. for images) + * @param peakpicker Shall the applet be used as a peak selection tool (see peakpicker.html in demo)? */ ! public NmrDetailSpectrum(SpectrumModel model, AbstractDataContainer l, boolean isgraphic, boolean peakpicker) { ! super(model, l,peakpicker); init(l); this.isgraphic = isgraphic; *************** *** 550,552 **** --- 563,603 ---- zoom(metrics.getXminInitial(), metrics.getXmaxInitial()); } + + /** + * Does a peakpicking in the given range + * @param mouseX mose position x + * @param mouseY mose position y + */ + public void pickpeaks(double startX, double endX){ + double sum=0; + int numberpeaks=0; + for(int i=0;i<pList.getAllPeaks(false).length;i++){ + if(pList.getAllPeaks(false)[i].getValueX()>=startX && pList.getAllPeaks(false)[i].getValueX()<=endX){ + sum+=pList.getAllPeaks(false)[i].getValueX(); + numberpeaks++; + } + } + double newpeak=((int)(sum/numberpeaks*100))/100d; + pickedPeaks.add(new Double(newpeak)); + if(listmodel!=null) + listmodel.addElement(new String(newpeak+"")); + } + + /** + * Returns the peaks in case the applet was used as a peak selection tool (see peakpicer.html in demo) + * + * @return The peaks + */ + public ArrayList getPickedPeaks(){ + return pickedPeaks; + } + + /** + * Sets a defaultListModel for a JList in the main window to show the selected peaks + * + * @param listmodel The listmodel + */ + public void setListModel(DefaultListModel listmodel){ + this.listmodel=listmodel; + } } Index: NmrNavigationSpectrum.java =================================================================== RCS file: /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer/nmr/NmrNavigationSpectrum.java,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -r1.2 -r1.3 *** NmrNavigationSpectrum.java 11 Dec 2006 15:52:29 -0000 1.2 --- NmrNavigationSpectrum.java 4 Apr 2007 15:32:43 -0000 1.3 *************** *** 46,51 **** */ public NmrNavigationSpectrum(SpectrumModel model, AbstractDataContainer l, SpectrumNavigation sn) { ! super(model, l); ! init(l); this.specNav=sn; } --- 46,51 ---- */ public NmrNavigationSpectrum(SpectrumModel model, AbstractDataContainer l, SpectrumNavigation sn) { ! super(model, l,false); ! init(l,false); this.specNav=sn; } *************** *** 57,62 **** */ public NmrNavigationSpectrum(SpectrumModel model, AbstractDataContainer l) { ! super(model, l); ! init(l); this.specNav=null; } --- 57,62 ---- */ public NmrNavigationSpectrum(SpectrumModel model, AbstractDataContainer l) { ! super(model, l,false); ! init(l,false); this.specNav=null; } *************** *** 65,70 **** /** * Init spectrum */ ! protected void init(AbstractDataContainer data) { double min = data.getXmin(); double max = data.getXmax(); --- 65,73 ---- /** * Init spectrum + * + * @param data list of peaks + * @param peakpicker Shall the applet be used as a peak selection tool (see peakpicker.html in demo)? */ ! protected void init(AbstractDataContainer data, boolean peakpicker) { double min = data.getXmin(); double max = data.getXmax(); Index: NmrRawDataDetailSpectrum.java =================================================================== RCS file: /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer/nmr/NmrRawDataDetailSpectrum.java,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -r1.2 -r1.3 *** NmrRawDataDetailSpectrum.java 5 Jul 2005 08:01:03 -0000 1.2 --- NmrRawDataDetailSpectrum.java 4 Apr 2007 15:32:43 -0000 1.3 *************** *** 42,48 **** * @param l list of peaks * @param isgraphic flag used to paint graphic (e.g. for images) */ ! public NmrRawDataDetailSpectrum(SpectrumModel model, AbstractDataContainer l, boolean isgraphic) { ! super(model, l); init(); this.isgraphic = isgraphic; --- 42,49 ---- * @param l list of peaks * @param isgraphic flag used to paint graphic (e.g. for images) + * @param peakpicker Shall the applet be used as a peak selection tool (see peakpicker.html in demo)? */ ! public NmrRawDataDetailSpectrum(SpectrumModel model, AbstractDataContainer l, boolean isgraphic, boolean peakpicker) { ! super(model, l, peakpicker); init(); this.isgraphic = isgraphic; Index: NmrSpecRenderer.java =================================================================== RCS file: /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer/nmr/NmrSpecRenderer.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -r1.1 -r1.2 *** NmrSpecRenderer.java 28 Jun 2005 14:41:38 -0000 1.1 --- NmrSpecRenderer.java 4 Apr 2007 15:32:43 -0000 1.2 *************** *** 19,27 **** package org.openscience.nmrshiftdb.spectrumapplet.renderer.nmr; ! import org.openscience.nmrshiftdb.spectrumapplet.data.nmr.*; ! import org.openscience.nmrshiftdb.spectrumapplet.renderer.*; ! import org.openscience.nmrshiftdb.spectrumapplet.renderer.dialog.*; ! import java.awt.*; /** --- 19,28 ---- package org.openscience.nmrshiftdb.spectrumapplet.renderer.nmr; ! import java.awt.Cursor; ! import java.util.ArrayList; ! import org.openscience.nmrshiftdb.spectrumapplet.data.nmr.NmrPeak; ! import org.openscience.nmrshiftdb.spectrumapplet.renderer.SpectrumRenderer; ! import org.openscience.nmrshiftdb.spectrumapplet.renderer.dialog.AbstractDialog; /** *************** *** 117,119 **** --- 118,134 ---- */ public void leftReleased(int mouseX, int mouseY); + + /** + * Does a peakpicking in the given range + * @param mouseX mose position x + * @param mouseY mose position y + */ + public void pickpeaks(double startX, double endX); + + /** + * Returns the peaks in case the applet was used as a peak selection tool (see peakpicer.html in demo) + * + * @return The peaks + */ + public ArrayList getPickedPeaks(); } |
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From: Stefan K. <sh...@us...> - 2007-04-04 15:32:49
|
Update of /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv16960/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer Modified Files: SpectrumControler.java SpectrumNavigation.java SpectrumRenderer.java Log Message: added a facility to manually select peaks from e. g. a proton spectrum with many peaks Index: SpectrumControler.java =================================================================== RCS file: /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer/SpectrumControler.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -r1.1 -r1.2 *** SpectrumControler.java 28 Jun 2005 14:41:36 -0000 1.1 --- SpectrumControler.java 4 Apr 2007 15:32:43 -0000 1.2 *************** *** 22,25 **** --- 22,26 ---- import java.awt.*; + import java.util.ArrayList; /** *************** *** 145,147 **** --- 146,155 ---- */ public void toggleCorrelation(); + + /** + * Returns the peaks in case the applet was used as a peak selection tool (see peakpicer.html in demo) + * + * @return The peaks + */ + public ArrayList getPickedPeaks(); } Index: SpectrumNavigation.java =================================================================== RCS file: /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer/SpectrumNavigation.java,v retrieving revision 1.8 retrieving revision 1.9 diff -C2 -r1.8 -r1.9 *** SpectrumNavigation.java 11 Dec 2006 15:52:29 -0000 1.8 --- SpectrumNavigation.java 4 Apr 2007 15:32:43 -0000 1.9 *************** *** 28,35 **** --- 28,43 ---- import java.awt.Graphics2D; import java.awt.Panel; + import java.awt.ScrollPane; + import java.awt.event.ActionEvent; + import java.awt.event.ActionListener; import java.awt.event.KeyAdapter; import java.awt.event.KeyEvent; + import java.util.ArrayList; + import javax.swing.DefaultListModel; import javax.swing.JApplet; + import javax.swing.JButton; + import javax.swing.JLabel; + import javax.swing.JList; import javax.swing.JPanel; *************** *** 75,78 **** --- 83,91 ---- private CorrelationControler corrCalc; JExternalFrame jexf = null; + private boolean peakpicker=false; + private ScrollPane sp; + DefaultListModel listModel; + JList peaklist; + /** *************** *** 89,94 **** public SpectrumNavigation(String specType, String specFrequency, String solvent, String predictSpec, String predictionHistogram, String experimentalSpec, SpectrumModel model, ! SpectrumApplet a, boolean isgraphic) { boolean unknownFreq = false; if (specType == null || specType.length() == 0 || !specType.trim().equals(NmrData.SPECTRUM_1H)) { specType = DataContainer.SPECTRUM_13C; --- 102,108 ---- public SpectrumNavigation(String specType, String specFrequency, String solvent, String predictSpec, String predictionHistogram, String experimentalSpec, SpectrumModel model, ! SpectrumApplet a, boolean isgraphic, boolean peakpicker) { boolean unknownFreq = false; + this.peakpicker=peakpicker; if (specType == null || specType.length() == 0 || !specType.trim().equals(NmrData.SPECTRUM_1H)) { specType = DataContainer.SPECTRUM_13C; *************** *** 119,123 **** pExp.setSpectrumProperty(pExp.UNKNOWN_FREQ, String.valueOf(unknownFreq)); } ! init(pPredicted, pExp, model, a, isgraphic); } --- 133,137 ---- pExp.setSpectrumProperty(pExp.UNKNOWN_FREQ, String.valueOf(unknownFreq)); } ! init(pPredicted, pExp, model, a, isgraphic, peakpicker); } *************** *** 134,139 **** */ public SpectrumNavigation(String specType, String specFrequency, String solvent, String predictSpec, ! String predictionHistogram, String experimentalSpec, SpectrumApplet a, boolean isgraphic) { ! this(specType, specFrequency, solvent, predictSpec, predictionHistogram, experimentalSpec, null, a, isgraphic); } --- 148,153 ---- */ public SpectrumNavigation(String specType, String specFrequency, String solvent, String predictSpec, ! String predictionHistogram, String experimentalSpec, SpectrumApplet a, boolean isgraphic, boolean peakpicker) { ! this(specType, specFrequency, solvent, predictSpec, predictionHistogram, experimentalSpec, null, a, isgraphic,peakpicker); } *************** *** 147,155 **** */ public SpectrumNavigation(AbstractDataContainer p, SpectrumModel m, SpectrumApplet a, boolean isgraphic) { ! init(p, null, m, a, isgraphic); } private SpectrumRenderer initRenderer(AbstractDataContainer dc, SpectrumModel m, ! boolean isNavigationSpec, boolean setExtendedOptionDialog, boolean isgraphic) { SpectrumRenderer r = null; boolean is13C = dc.is13Cspectrum(); --- 161,169 ---- */ public SpectrumNavigation(AbstractDataContainer p, SpectrumModel m, SpectrumApplet a, boolean isgraphic) { ! init(p, null, m, a, isgraphic,false); } private SpectrumRenderer initRenderer(AbstractDataContainer dc, SpectrumModel m, ! boolean isNavigationSpec, boolean setExtendedOptionDialog, boolean isgraphic, boolean peakpicker) { SpectrumRenderer r = null; boolean is13C = dc.is13Cspectrum(); *************** *** 170,174 **** m.setLineWidth(CommonUtils.getNumberProperty("lw(1H)", 0.5)); } ! r = new NmrDetailSpectrum(m, dc, isgraphic); if (isNavigationSpec) { r = new NmrNavigationSpectrum(m, dc,this); --- 184,188 ---- m.setLineWidth(CommonUtils.getNumberProperty("lw(1H)", 0.5)); } ! r = new NmrDetailSpectrum(m, dc, isgraphic,peakpicker); if (isNavigationSpec) { r = new NmrNavigationSpectrum(m, dc,this); *************** *** 191,195 **** } else { ! r = new NmrRawDataDetailSpectrum(m, dc, isgraphic); } } --- 205,209 ---- } else { ! r = new NmrRawDataDetailSpectrum(m, dc, isgraphic,peakpicker); } } *************** *** 216,220 **** */ private void init(AbstractDataContainer pPrediction, AbstractDataContainer pExperimental, ! SpectrumModel model, SpectrumApplet a, boolean isgraphic) { applet = a; SpectrumModel mPred = model; --- 230,234 ---- */ private void init(AbstractDataContainer pPrediction, AbstractDataContainer pExperimental, ! SpectrumModel model, SpectrumApplet a, boolean isgraphic, boolean peakpicker) { applet = a; SpectrumModel mPred = model; *************** *** 237,241 **** //initialize predicted spectrum display: ! sprPrediction = initRenderer(pPrediction, mPred, false, true, isgraphic); //initialize experimental spectrum display: if (pExperimental != null) { --- 251,255 ---- //initialize predicted spectrum display: ! sprPrediction = initRenderer(pPrediction, mPred, false, true, isgraphic, peakpicker); //initialize experimental spectrum display: if (pExperimental != null) { *************** *** 248,257 **** pNavigation = pExperimental; } ! sprExperimental = initRenderer(pExperimental, mExp, false, true, isgraphic); } //initialize navigation spectrum display: SpectrumModel mNav = new SpectrumModel(); ! nav = initRenderer(pNavigation, mNav, true, false, isgraphic); ((Component) nav).setVisible(mPred.isShowNavigationView()); if ((sprExperimental != null) && (sprExperimental instanceof NmrDetailSpectrum) && --- 262,271 ---- pNavigation = pExperimental; } ! sprExperimental = initRenderer(pExperimental, mExp, false, true, isgraphic, peakpicker); } //initialize navigation spectrum display: SpectrumModel mNav = new SpectrumModel(); ! nav = initRenderer(pNavigation, mNav, true, false, isgraphic,peakpicker); ((Component) nav).setVisible(mPred.isShowNavigationView()); if ((sprExperimental != null) && (sprExperimental instanceof NmrDetailSpectrum) && *************** *** 260,268 **** (NmrDetailSpectrum) sprExperimental); } ! initGraphic(); } ! private void initGraphic() { setLayout(new FlowLayout()); Panel outerpanel=new Panel(); --- 274,282 ---- (NmrDetailSpectrum) sprExperimental); } ! initGraphic(peakpicker); } ! private void initGraphic(boolean peakpicker) { setLayout(new FlowLayout()); Panel outerpanel=new Panel(); *************** *** 283,286 **** --- 297,322 ---- sprPrediction.getMetrics().getXmaxInitial()); } + if(peakpicker){ + listModel = new DefaultListModel(); + if(sprPrediction instanceof NmrDetailSpectrum) + ((NmrDetailSpectrum)sprPrediction).setListModel(listModel); + peaklist=new JList(listModel); + sp=new ScrollPane(ScrollPane.SCROLLBARS_AS_NEEDED); + sp.add(peaklist); + JPanel panel=new JPanel(); + panel.setLayout(new BorderLayout()); + panel.add(sp,BorderLayout.CENTER); + JLabel label=new JLabel("Selected Peaks:"); + panel.add(label,BorderLayout.NORTH); + JButton button=new JButton("Delete Peak"); + panel.add(button,BorderLayout.SOUTH); + button.addActionListener(new ActionListener() { + public void actionPerformed(ActionEvent e) { + sprPrediction.getPickedPeaks().remove(peaklist.getSelectedIndex()); + listModel.remove(peaklist.getSelectedIndex()); + } + }); + outerpanel.add(panel,BorderLayout.EAST); + } } *************** *** 426,429 **** --- 462,467 ---- int h = size.height; int w = size.width; + if(peakpicker) + w-=100; if (h != 0) { if (h < 530) { *************** *** 435,454 **** } Dimension dd = new Dimension(w, min); if (!((Component) nav).isVisible()) { min = 0; //dd = new Dimension(0, 0); } ! setSize(nav, dd); if (sprExperimental != null) { int z = ((h - min) / 2); Dimension d1 = new Dimension(w, z); ! setSize(sprExperimental, d1); z = (h - min) - z; Dimension d2 = new Dimension(w, z); ! setSize(sprPrediction, d2); } else { Dimension d2 = new Dimension(w, h - min); ! setSize(sprPrediction, d2); } --- 473,493 ---- } Dimension dd = new Dimension(w, min); + Dimension peaklistd=new Dimension(100,min); if (!((Component) nav).isVisible()) { min = 0; //dd = new Dimension(0, 0); } ! setSize(nav, dd,peaklistd); if (sprExperimental != null) { int z = ((h - min) / 2); Dimension d1 = new Dimension(w, z); ! setSize(sprExperimental, d1,peaklistd); z = (h - min) - z; Dimension d2 = new Dimension(w, z); ! setSize(sprPrediction, d2,peaklistd); } else { Dimension d2 = new Dimension(w, h - min); ! setSize(sprPrediction, d2,peaklistd); } *************** *** 458,466 **** ! private void setSize(SpectrumRenderer r, Dimension d) { ((AbstractRenderer) r).setSize(d); ((AbstractRenderer) r).setMinimumSize(d); ((AbstractRenderer) r).setMaximumSize(d); ((AbstractRenderer) r).setPreferredSize(d); } --- 497,509 ---- ! private void setSize(SpectrumRenderer r, Dimension d, Dimension d2) { ((AbstractRenderer) r).setSize(d); ((AbstractRenderer) r).setMinimumSize(d); ((AbstractRenderer) r).setMaximumSize(d); ((AbstractRenderer) r).setPreferredSize(d); + sp.setSize(d2); + sp.setMinimumSize(d2); + sp.setMaximumSize(d2); + sp.setPreferredSize(d2); } *************** *** 649,651 **** --- 692,703 ---- return jexf; } + + /** + * Returns the peaks in case the applet was used as a peak selection tool (see peakpicer.html in demo) + * + * @return The peaks + */ + public ArrayList getPickedPeaks(){ + return sprPrediction.getPickedPeaks(); + } } Index: SpectrumRenderer.java =================================================================== RCS file: /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer/SpectrumRenderer.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -r1.1 -r1.2 *** SpectrumRenderer.java 28 Jun 2005 14:41:36 -0000 1.1 --- SpectrumRenderer.java 4 Apr 2007 15:32:43 -0000 1.2 *************** *** 19,27 **** package org.openscience.nmrshiftdb.spectrumapplet.renderer; ! import org.openscience.nmrshiftdb.spectrumapplet.data.*; ! import org.openscience.nmrshiftdb.spectrumapplet.renderer.painter.*; ! import java.awt.*; ! import java.awt.event.*; /** --- 19,29 ---- package org.openscience.nmrshiftdb.spectrumapplet.renderer; ! import java.awt.Color; ! import java.awt.Graphics; ! import java.awt.event.KeyEvent; ! import java.util.ArrayList; ! import org.openscience.nmrshiftdb.spectrumapplet.data.DataContainer; ! import org.openscience.nmrshiftdb.spectrumapplet.renderer.painter.CurvePainter; /** *************** *** 151,153 **** --- 153,162 ---- */ public void keyPressed(KeyEvent e); + + /** + * Returns the peaks in case the applet was used as a peak selection tool (see peakpicer.html in demo) + * + * @return The peaks + */ + public ArrayList getPickedPeaks(); } |
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From: Stefan K. <sh...@us...> - 2007-04-04 15:32:49
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Update of /cvsroot/nmrshiftdb/spectrumapplet/src/java/tests/org/openscience/nmrshiftdb/spectrumapplet/renderer In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv16960/src/java/tests/org/openscience/nmrshiftdb/spectrumapplet/renderer Modified Files: RendererTest.java Log Message: added a facility to manually select peaks from e. g. a proton spectrum with many peaks Index: RendererTest.java =================================================================== RCS file: /cvsroot/nmrshiftdb/spectrumapplet/src/java/tests/org/openscience/nmrshiftdb/spectrumapplet/renderer/RendererTest.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -r1.1 -r1.2 *** RendererTest.java 28 Jun 2005 14:41:40 -0000 1.1 --- RendererTest.java 4 Apr 2007 15:32:44 -0000 1.2 *************** *** 24,28 **** frame = new JFrame("SpectraRendererTest"); frame.getContentPane().setLayout(new BorderLayout()); ! sn = new SpectrumNavigation(specType, freq, solvent, predictSpec, prediction, expSpectrum, model, null, isgraphic); activateKeyListener(frame, sn.getDetailSpectrums()[0]); frame.getContentPane().add(sn, BorderLayout.CENTER); --- 24,28 ---- frame = new JFrame("SpectraRendererTest"); frame.getContentPane().setLayout(new BorderLayout()); ! sn = new SpectrumNavigation(specType, freq, solvent, predictSpec, prediction, expSpectrum, model, null, isgraphic,false); activateKeyListener(frame, sn.getDetailSpectrums()[0]); frame.getContentPane().add(sn, BorderLayout.CENTER); |
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From: Stefan K. <sh...@us...> - 2007-04-04 15:32:49
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Update of /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer/action In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv16960/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer/action Modified Files: NavSpectrumMouseActions.java SpectrumMouseActions.java Log Message: added a facility to manually select peaks from e. g. a proton spectrum with many peaks Index: NavSpectrumMouseActions.java =================================================================== RCS file: /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer/action/NavSpectrumMouseActions.java,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -r1.2 -r1.3 *** NavSpectrumMouseActions.java 11 Dec 2006 15:52:29 -0000 1.2 --- NavSpectrumMouseActions.java 4 Apr 2007 15:32:43 -0000 1.3 *************** *** 98,103 **** public void mouseDragged(MouseEvent e) { if (isRightPressed) { ! renderer.getZoomMarker().setDraggedLimit(e.getX()); ! renderer.getZoomMarker().paintMarker(true); } else if (isLeftPressed) { --- 98,103 ---- public void mouseDragged(MouseEvent e) { if (isRightPressed) { ! renderer.getZoomMarker().setDraggedLimit(e.getX()); ! renderer.getZoomMarker().paintMarker(true); } else if (isLeftPressed) { Index: SpectrumMouseActions.java =================================================================== RCS file: /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer/action/SpectrumMouseActions.java,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -r1.2 -r1.3 *** SpectrumMouseActions.java 11 Dec 2006 15:52:29 -0000 1.2 --- SpectrumMouseActions.java 4 Apr 2007 15:32:43 -0000 1.3 *************** *** 40,50 **** private boolean ignoreZoomOps; private int oldX; /** * Creates a new instance of SpectrumMouseActions * @param r the spectrum renderer */ ! public SpectrumMouseActions(NmrSpecRenderer r) { renderer = r; } --- 40,53 ---- private boolean ignoreZoomOps; private int oldX; + private boolean peakpicker; /** * Creates a new instance of SpectrumMouseActions * @param r the spectrum renderer + * @param peakpicker Shall the applet be used as a peak selection tool (see peakpicker.html in demo)? */ ! public SpectrumMouseActions(NmrSpecRenderer r, boolean peakpicker) { renderer = r; + this.peakpicker=peakpicker; } *************** *** 113,120 **** double[] r = renderer.getZoomMarker().getRange(); renderer.zoom(r[0], r[1]); } else if (isLeftPressed) { ! isLeftPressed = false; ! renderer.leftReleased(0, 0); } } --- 116,130 ---- double[] r = renderer.getZoomMarker().getRange(); renderer.zoom(r[0], r[1]); + } else if (isLeftPressed) { ! if(!peakpicker){ ! isLeftPressed = false; ! renderer.leftReleased(0, 0); ! }else{ ! renderer.getZoomMarker().setDraggedLimit(e.getX()); ! double[] r = renderer.getZoomMarker().getRange(); ! renderer.pickpeaks(r[0],r[1]); ! } } } |
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From: Stefan K. <sh...@us...> - 2007-04-04 15:32:48
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Update of /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer/ir In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv16960/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer/ir Modified Files: IrRawDataDetailSpectrum.java Log Message: added a facility to manually select peaks from e. g. a proton spectrum with many peaks Index: IrRawDataDetailSpectrum.java =================================================================== RCS file: /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer/ir/IrRawDataDetailSpectrum.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -r1.1 -r1.2 *** IrRawDataDetailSpectrum.java 28 Jun 2005 14:41:37 -0000 1.1 --- IrRawDataDetailSpectrum.java 4 Apr 2007 15:32:43 -0000 1.2 *************** *** 43,47 **** */ public IrRawDataDetailSpectrum(SpectrumModel model, AbstractDataContainer l) { ! super(model, l, true); init(); } --- 43,47 ---- */ public IrRawDataDetailSpectrum(SpectrumModel model, AbstractDataContainer l) { ! super(model, l,false,false); init(); } |
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From: Stefan K. <sh...@us...> - 2007-04-04 15:32:48
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Update of /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv16960/src/java/org/openscience/nmrshiftdb/spectrumapplet Modified Files: SpectrumViewNoRenderer.java Log Message: added a facility to manually select peaks from e. g. a proton spectrum with many peaks Index: SpectrumViewNoRenderer.java =================================================================== RCS file: /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/SpectrumViewNoRenderer.java,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -r1.3 -r1.4 *** SpectrumViewNoRenderer.java 10 Oct 2006 15:15:30 -0000 1.3 --- SpectrumViewNoRenderer.java 4 Apr 2007 15:32:43 -0000 1.4 *************** *** 28,31 **** --- 28,32 ---- import java.awt.event.WindowAdapter; import java.awt.event.WindowEvent; + import java.util.ArrayList; import javax.swing.JApplet; *************** *** 67,71 **** String solvent = getParameter(APPLET_PARAM[4]); String expSpec = getParameter(APPLET_PARAM[5]); ! spectrumPanel = new SpectrumNavigation(specType, f, solvent, predSpec, pred, expSpec, this, false); readParameter(); //activateKeyListener(); --- 68,73 ---- String solvent = getParameter(APPLET_PARAM[4]); String expSpec = getParameter(APPLET_PARAM[5]); ! String peakPicker= getParameter("peakpicker"); ! spectrumPanel = new SpectrumNavigation(specType, f, solvent, predSpec, pred, expSpec, this, false, peakPicker!=null && peakPicker.equals("true")); readParameter(); //activateKeyListener(); *************** *** 147,150 **** */ public void removeHighlightingInStructur() { ! } } --- 149,165 ---- */ public void removeHighlightingInStructur() { ! } ! ! /** ! * Returns the peaks in case the applet was used as a peak selection tool (see peakpicer.html in demo) ! * ! * @return The peaks ! */ ! public String getPickedPeaks(){ ! StringBuffer sb=new StringBuffer(); ! for(int i=0;i<spectrumPanel.getPickedPeaks().size();i++){ ! sb.append((Double)spectrumPanel.getPickedPeaks().get(i)+"|"); ! } ! return sb.toString(); ! } } |
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From: Stefan K. <sh...@us...> - 2007-04-03 14:49:20
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Update of /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv901/src/java/org/openscience/nmrshiftdb/spectrumapplet Modified Files: SpectrumView.java Log Message: the path to the plugin.jar must be in classpath - no idea why it wasn't Index: SpectrumView.java =================================================================== RCS file: /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/SpectrumView.java,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -r1.4 -r1.5 *** SpectrumView.java 8 Dec 2006 15:19:18 -0000 1.4 --- SpectrumView.java 3 Apr 2007 14:48:29 -0000 1.5 *************** *** 76,80 **** JSObject tr = (JSObject) win.eval("document.getElementById(\"tableid"+(oldnumbers[i]-1)+"\").style"); if((oldnumbers[i]+1)%2==0) ! tr.setMember("bgColor","white"); else tr.setMember("backgroundColor","#D3D3D3"); --- 76,80 ---- JSObject tr = (JSObject) win.eval("document.getElementById(\"tableid"+(oldnumbers[i]-1)+"\").style"); if((oldnumbers[i]+1)%2==0) ! tr.setMember("backgroundColor","white"); else tr.setMember("backgroundColor","#D3D3D3"); |
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From: Stefan K. <sh...@us...> - 2007-04-03 14:49:13
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Update of /cvsroot/nmrshiftdb/spectrumapplet In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv901 Modified Files: build.xml Log Message: the path to the plugin.jar must be in classpath - no idea why it wasn't Index: build.xml =================================================================== RCS file: /cvsroot/nmrshiftdb/spectrumapplet/build.xml,v retrieving revision 1.12 retrieving revision 1.13 diff -C2 -r1.12 -r1.13 *** build.xml 11 Dec 2006 15:52:28 -0000 1.12 --- build.xml 3 Apr 2007 14:48:28 -0000 1.13 *************** *** 15,18 **** --- 15,19 ---- <include name="*.jar" /> </fileset> + <pathelement location="/usr/lib/j2sdk1.5-sun/jre/lib/plugin.jar"/> </path> *************** *** 44,48 **** <delete file="${srcTemp}/MarvinWrapper.java"/> <delete file="${srcTemp}/SpectrumView.java"/> ! <javac srcdir="${srcTemp}" destdir="${build}" target="1.2" optimize="off" debug="on" deprecation="on" source="1.2"> <classpath refid="project.class.path" /> </javac> --- 45,49 ---- <delete file="${srcTemp}/MarvinWrapper.java"/> <delete file="${srcTemp}/SpectrumView.java"/> ! <javac srcdir="${srcTemp}" destdir="${build}" target="1.2" optimize="on" debug="off" deprecation="on" source="1.2"> <classpath refid="project.class.path" /> </javac> |
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From: Stefan K. <sh...@us...> - 2006-12-11 15:52:38
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Update of /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv22721/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer Modified Files: SpectrumNavigation.java Log Message: reset of zoom and undocking should be possible Index: SpectrumNavigation.java =================================================================== RCS file: /cvsroot/nmrshiftdb/spectrumapplet/src/java/org/openscience/nmrshiftdb/spectrumapplet/renderer/SpectrumNavigation.java,v retrieving revision 1.7 retrieving revision 1.8 diff -C2 -r1.7 -r1.8 *** SpectrumNavigation.java 8 Dec 2006 12:57:19 -0000 1.7 --- SpectrumNavigation.java 11 Dec 2006 15:52:29 -0000 1.8 *************** *** 23,27 **** import java.awt.Color; import java.awt.Component; - import java.awt.Container; import java.awt.Dimension; import java.awt.FlowLayout; --- 23,26 ---- *************** *** 31,40 **** import java.awt.event.KeyAdapter; import java.awt.event.KeyEvent; - import java.awt.event.MouseAdapter; - import java.awt.event.MouseEvent; - import java.awt.event.MouseListener; import javax.swing.JApplet; - import javax.swing.JFrame; import javax.swing.JPanel; --- 30,35 ---- *************** *** 177,181 **** r = new NmrDetailSpectrum(m, dc, isgraphic); if (isNavigationSpec) { ! r = new NmrNavigationSpectrum(m, dc); } if (setExtendedOptionDialog) { --- 172,176 ---- r = new NmrDetailSpectrum(m, dc, isgraphic); if (isNavigationSpec) { ! r = new NmrNavigationSpectrum(m, dc,this); } if (setExtendedOptionDialog) { *************** *** 288,296 **** sprPrediction.getMetrics().getXmaxInitial()); } - MouseListener popupListener = new PopupListener(this); - ((AbstractRenderer)sprPrediction).addMouseListener(popupListener); - if (sprExperimental != null) { - ((AbstractRenderer)sprExperimental).addMouseListener(popupListener); - } } --- 283,286 ---- *************** *** 654,691 **** * @return Returns the jexf. */ ! private JExternalFrame getJexf() { if (jexf == null) jexf = new JExternalFrame(); return jexf; } - - - /** - * For detaching - * - */ - public class PopupListener extends MouseAdapter { - - SpectrumNavigation panel; - Container parent; - JFrame frame = new JFrame("SpectrumApplet window"); - - - public PopupListener(SpectrumNavigation panel){ - this.panel = panel; - } - - /** - * Description of the Method - * - *@param e Description of the Parameter - */ - public void mousePressed(MouseEvent e) { - if (e.getButton() == 1 && e.getClickCount() == 2) { - if (!getJexf().isShowing()) { - getJexf().show(panel); - } - } - } - } } --- 644,651 ---- * @return Returns the jexf. */ ! public JExternalFrame getJexf() { if (jexf == null) jexf = new JExternalFrame(); return jexf; } } |
