001/* 002 * BioJava development code 003 * 004 * This code may be freely distributed and modified under the 005 * terms of the GNU Lesser General Public Licence. This should 006 * be distributed with the code. If you do not have a copy, 007 * see: 008 * 009 * http://www.gnu.org/copyleft/lesser.html 010 * 011 * Copyright for this code is held jointly by the individual 012 * authors. These should be listed in @author doc comments. 013 * 014 * For more information on the BioJava project and its aims, 015 * or to join the biojava-l mailing list, visit the home page 016 * at: 017 * 018 * http://www.biojava.org/ 019 * 020 */ 021package org.biojava.nbio.structure.align.ce; 022 023import org.biojava.nbio.structure.Atom; 024import org.biojava.nbio.structure.Group; 025import org.biojava.nbio.structure.Structure; 026import org.biojava.nbio.structure.align.model.AFPChain; 027import org.biojava.nbio.structure.align.util.UserConfiguration; 028import org.biojava.nbio.structure.jama.Matrix; 029 030import javax.swing.*; 031import java.io.File; 032import java.lang.reflect.InvocationTargetException; 033import java.lang.reflect.Method; 034import java.util.List; 035 036/** A class to wrap some of the strucutre.gui classes using Reflection 037 * 038 * @author Andreas Prlic 039 * 040 */ 041 042public class GuiWrapper { 043 044 static final String guiPackage = "org.biojava.nbio.structure.gui"; 045 046 static final String strucAlignmentDisplay = "org.biojava.nbio.structure.align.gui.StructureAlignmentDisplay"; 047 static final String displayAFP = "org.biojava.nbio.structure.align.gui.DisplayAFP" ; 048 static final String alignmentGUI = "org.biojava.nbio.structure.align.gui.AlignmentGui"; 049 static final String strucAligJmol = "org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol"; 050 static final String abstractAligJmol = "org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol"; 051 052 static final String scaleMatrixPanel = "org.biojava.nbio.structure.gui.ScaleableMatrixPanel"; 053 054 @SuppressWarnings("rawtypes") 055 public static boolean isGuiModuleInstalled(){ 056 String className = displayAFP; 057 try { 058 @SuppressWarnings("unused") 059 Class c = Class.forName(className); 060 } catch (ClassNotFoundException ex){ 061 return false; 062 } 063 return true; 064 } 065 066 @SuppressWarnings({ "rawtypes", "unchecked" }) 067 public static Object display(AFPChain afpChain, Atom[] ca1, Atom[] ca2) 068 throws ClassNotFoundException, NoSuchMethodException, InvocationTargetException, IllegalAccessException{ 069 070 Class c = Class.forName(strucAlignmentDisplay); 071 072 Method display = c.getMethod("display", new Class[]{AFPChain.class, Atom[].class, 073 Atom[].class}); 074 075 Object structureAlignmentJmol = display.invoke(null, afpChain,ca1,ca2); 076 077 return structureAlignmentJmol; 078 } 079 080 081 082 @SuppressWarnings({ "rawtypes", "unchecked" }) 083 public static void showAlignmentImage(AFPChain afpChain, Atom[] ca1, 084 Atom[] ca2, Object jmol) 085 throws ClassNotFoundException, NoSuchMethodException, InvocationTargetException, IllegalAccessException{ 086 087 Class abstractAligJmolC = Class.forName(abstractAligJmol); 088 089 Class c = Class.forName(displayAFP); 090 Method show = c.getMethod("showAlignmentPanel", new Class[] {AFPChain.class, Atom[].class, Atom[].class, abstractAligJmolC}); 091 092 show.invoke(null,afpChain, ca1, ca2, jmol); 093 } 094 095 096 /** Shows a structure in Jmol 097 * @since 3.0.5 098 */ 099 public static void showStructure(Structure structure) 100 throws ClassNotFoundException, NoSuchMethodException, 101 InvocationTargetException, IllegalAccessException, InstantiationException{ 102 103 Class<?> structureAlignmentJmol = Class.forName(strucAligJmol); 104 105 Object strucAligJ = structureAlignmentJmol.newInstance(); 106 107 Method setS = structureAlignmentJmol.getMethod("setStructure", new Class[] {Structure.class}); 108 109 setS.invoke(strucAligJ,structure); 110 } 111 112 113 @SuppressWarnings({ "rawtypes", "unchecked" }) 114 public static void showAlignmentGUI() 115 throws ClassNotFoundException, NoSuchMethodException, InvocationTargetException, IllegalAccessException { 116 // proxy for AlignmentGui.getInstance(); 117 118 119 Class c = Class.forName(alignmentGUI); 120 Method m = c.getMethod("getInstance", (Class[])null); 121 m.invoke(c,(Object[])null); 122 } 123 124 @SuppressWarnings({"unused" }) 125 public static Structure getAlignedStructure(Atom[] ca1, Atom[] ca2) 126 throws ClassNotFoundException, NoSuchMethodException, 127 InvocationTargetException, IllegalAccessException{ 128 129 Class<?> structureAlignmentJmol = Class.forName(strucAligJmol); 130 131 Class<?> c = Class.forName(displayAFP); 132 Method show = c.getMethod("getAlignedStructure", new Class[] { Atom[].class, Atom[].class}); 133 134 Structure s = (Structure) show.invoke(null, ca1, ca2); 135 136 return s; 137 138 } 139 140 public static JPanel getScaleableMatrixPanel(Matrix m) 141 throws ClassNotFoundException, NoSuchMethodException, 142 InvocationTargetException, IllegalAccessException, InstantiationException{ 143 144 Class<?> scaleMatrixPanelC = Class.forName(scaleMatrixPanel); 145 146 Method setMatrix = scaleMatrixPanelC.getMethod("setMatrix", new Class[] { Matrix.class}); 147 148 JPanel panel = (JPanel) scaleMatrixPanelC.newInstance(); 149 150 setMatrix.invoke(panel, m); 151 152 return panel; 153 154 } 155 156 @SuppressWarnings({ "rawtypes", "unchecked", "unused" }) 157 public static Atom[] getAtomArray(Atom[] ca, List<Group> hetatoms, List<Group> nucs) 158 throws ClassNotFoundException, NoSuchMethodException, 159 InvocationTargetException, IllegalAccessException{ 160 161 Class structureAlignmentJmol = Class.forName(strucAligJmol); 162 163 Class c = Class.forName(displayAFP); 164 Method show = c.getMethod("getAtomArray", new Class[] { Atom[].class, List.class, List.class}); 165 166 Atom[] atoms = (Atom[]) show.invoke(null, ca, hetatoms, nucs); 167 168 return atoms; 169 170 } 171 172 /** 173 * @since 3.0.5 174 */ 175 public static void showDBResults(StartupParameters params) { 176 //System.err.println("not implemented full yet"); 177 178 // We want to do this, but because we don't know if structure-gui.jar is in the classpath we use reflection to hide the calls 179 180 UserConfiguration config = UserConfiguration.fromStartupParams(params); 181 182 String tableClass = "org.biojava.nbio.structure.align.gui.DBResultTable"; 183 184 try { 185 Class<?> c = Class.forName(tableClass); 186 Object table = c.newInstance(); 187 188 Method show = c.getMethod("show", new Class[]{File.class, UserConfiguration.class }); 189 190 show.invoke(table, new File(params.getShowDBresult()),config); 191 192 } catch (Exception e){ 193 e.printStackTrace(); 194 195 System.err.println("Probably structure-gui.jar is not in the classpath, can't show results..."); 196 } 197 198 //DBResultTable table = new DBResultTable(); 199 200 //table.show(new File(params.getShowDBresult()),config); 201 202 } 203 204}