Structure listener

diff --git a/src/jalview/structure/SequenceListener.java b/src/jalview/structure/SequenceListener.java
new file mode 100644 (file)
index 0000000..b4eefd6
--- /dev/null
+++ b/src/jalview/structure/SequenceListener.java
@@ -0,0 +1,30 @@
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
+ */\r
+package jalview.structure;\r
+\r
+import jalview.datamodel.*;\r
+\r
+public interface SequenceListener\r
+{\r
+  public void mouseOverSequence(SequenceI sequence, int index);\r
+\r
+  public void highlightSequence(jalview.datamodel.SequenceI seq, int index);\r
+\r
+  public void updateColours(SequenceI sequence, int index);\r
+}\r

diff --git a/src/jalview/structure/StructureListener.java b/src/jalview/structure/StructureListener.java
new file mode 100644 (file)
index 0000000..0d7819e
--- /dev/null
+++ b/src/jalview/structure/StructureListener.java
@@ -0,0 +1,30 @@
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
+ */\r
+package jalview.structure;\r
+\r
+public interface StructureListener\r
+{\r
+  public String getPdbFile();\r
+\r
+  public void mouseOverStructure(int atomIndex, String strInfo);\r
+\r
+  public void highlightAtom(int atomIndex, int pdbResNum, String chain, String pdbId);\r
+\r
+  public void updateColours(Object source);\r
+}\r

diff --git a/src/jalview/structure/StructureMapping.java b/src/jalview/structure/StructureMapping.java
new file mode 100644 (file)
index 0000000..06e6bc3
--- /dev/null
+++ b/src/jalview/structure/StructureMapping.java
@@ -0,0 +1,100 @@
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
+ */\r
+\r
+package jalview.structure;\r
+\r
+import jalview.datamodel.*;\r
+\r
+public class StructureMapping\r
+{\r
+  String mappingDetails;\r
+  SequenceI sequence;\r
+  String pdbfile;\r
+  String pdbid;\r
+  String pdbchain;\r
+\r
+  //Mapping index 0 is resNum, index 1 is atomNo\r
+  int[][] mapping;\r
+\r
+  public StructureMapping(SequenceI seq,\r
+                          String pdbfile,\r
+                          String pdbid,\r
+                          String chain,\r
+                          int[][] mapping,\r
+                          String mappingDetails)\r
+  {\r
+    sequence = seq;\r
+    this.pdbfile = pdbfile;\r
+    this.pdbid = pdbid;\r
+    this.pdbchain = chain;\r
+    this.mapping = mapping;\r
+    this.mappingDetails = mappingDetails;\r
+  }\r
+\r
+  public SequenceI getSequence()\r
+  {\r
+    return sequence;\r
+  }\r
+\r
+  public String getChain()\r
+  {\r
+    return pdbchain;\r
+  }\r
+\r
+  public String getPdbId()\r
+  {\r
+    return pdbid;\r
+  }\r
+\r
+  public int getAtomNum(int seqpos)\r
+  {\r
+    if (mapping.length > seqpos)\r
+    {\r
+      return mapping[seqpos][1];\r
+    }\r
+    else\r
+    {\r
+      return 0;\r
+    }\r
+  }\r
+\r
+  public int getPDBResNum(int seqpos)\r
+  {\r
+    if (mapping.length > seqpos)\r
+    {\r
+      return mapping[seqpos][0];\r
+    }\r
+    else\r
+    {\r
+      return 0;\r
+    }\r
+  }\r
+\r
+  public int getSeqPos(int pdbResNum)\r
+  {\r
+    for (int i = 0; i < mapping.length; i++)\r
+    {\r
+      if (mapping[i][0] == pdbResNum)\r
+      {\r
+        return i;\r
+      }\r
+    }\r
+    return -1;\r
+  }\r
+}\r

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
new file mode 100644 (file)
index 0000000..b4e63f4
--- /dev/null
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -0,0 +1,350 @@
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
+ */\r
+package jalview.structure;\r
+\r
+import java.io.*;\r
+import java.util.*;\r
+\r
+import MCview.*;\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
+\r
+public class StructureSelectionManager\r
+{\r
+  static StructureSelectionManager instance;\r
+  StructureMapping[] mappings;\r
+  Hashtable mappingData = new Hashtable();\r
+\r
+  public static StructureSelectionManager getStructureSelectionManager()\r
+  {\r
+    if (instance == null)\r
+    {\r
+      instance = new StructureSelectionManager();\r
+    }\r
+\r
+    return instance;\r
+  }\r
+\r
+  Vector listeners = new Vector();\r
+  public void addStructureViewerListener(Object svl)\r
+  {\r
+    if (!listeners.contains(svl))\r
+    {\r
+      listeners.addElement(svl);\r
+    }\r
+  }\r
+\r
+  public String alreadyMappedToFile(String pdbid)\r
+  {\r
+    if (mappings != null)\r
+    {\r
+      for (int i = 0; i < mappings.length; i++)\r
+      {\r
+        if (mappings[i].getPdbId().equals(pdbid))\r
+        {\r
+          return mappings[i].pdbfile;\r
+        }\r
+      }\r
+    }\r
+    return null;\r
+  }\r
+\r
+  /*\r
+     There will be better ways of doing this in the future, for now we'll use\r
+     the tried and tested MCview pdb mapping\r
+   */\r
+  public MCview.PDBfile setMapping(SequenceI[] sequence,\r
+                           String pdbFile,\r
+                           String protocol)\r
+  {\r
+    MCview.PDBfile pdb = null;\r
+    try\r
+    {\r
+      pdb = new MCview.PDBfile(pdbFile, protocol);\r
+    }\r
+    catch (Exception ex)\r
+    {\r
+      ex.printStackTrace();\r
+      return null;\r
+    }\r
+\r
+    for (int s = 0; s < sequence.length; s++)\r
+    {\r
+      String targetChain = "";\r
+\r
+      if (sequence[s].getName().indexOf("|") > -1)\r
+      {\r
+        targetChain = sequence[s].getName().substring(\r
+            sequence[s].getName().lastIndexOf("|") + 1);\r
+      }\r
+\r
+      int max = -10;\r
+      AlignSeq maxAlignseq = null;\r
+      String maxChainId = " ";\r
+      PDBChain maxChain = null;\r
+\r
+      for (int i = 0; i < pdb.chains.size(); i++)\r
+      {\r
+        AlignSeq as = new AlignSeq(sequence[s],\r
+                                   ( (PDBChain) pdb.chains.elementAt(i)).\r
+                                   sequence,\r
+                                   AlignSeq.PEP);\r
+        as.calcScoreMatrix();\r
+        as.traceAlignment();\r
+        PDBChain chain = ( (PDBChain) pdb.chains.elementAt(i));\r
+\r
+        if (as.maxscore > max\r
+            || (as.maxscore == max && chain.id.equals(targetChain)))\r
+        {\r
+          maxChain = chain;\r
+          max = as.maxscore;\r
+          maxAlignseq = as;\r
+          maxChainId = chain.id;\r
+        }\r
+      }\r
+\r
+      final StringBuffer mappingDetails = new StringBuffer();\r
+      mappingDetails.append("\n\nPDB Sequence is :\nSequence = " +\r
+                            maxChain.sequence.getSequenceAsString());\r
+      mappingDetails.append("\nNo of residues = " +\r
+                            maxChain.residues.\r
+                            size() +\r
+                            "\n\n");\r
+      PrintStream ps = new PrintStream(System.out)\r
+      {\r
+        public void print(String x)\r
+        {\r
+          mappingDetails.append(x);\r
+        }\r
+\r
+        public void println()\r
+        {\r
+          mappingDetails.append("\n");\r
+        }\r
+      };\r
+\r
+      maxAlignseq.printAlignment(ps);\r
+\r
+      mappingDetails.append("\nPDB start/end " + maxAlignseq.seq2start + " " +\r
+                            maxAlignseq.seq2end);\r
+      mappingDetails.append("\nSEQ start/end "\r
+                            + (maxAlignseq.seq1start + sequence[s].getStart() - 1) +\r
+                            " "\r
+                            + (maxAlignseq.seq1end + sequence[s].getEnd() - 1));\r
+\r
+      maxChain.makeExactMapping(maxAlignseq, sequence[s]);\r
+\r
+    //  maxChain.transferRESNUMFeatures(sequence[s], null);\r
+\r
+      int[][] mapping = new int[sequence[s].getEnd() + 2][2];\r
+      int resNum = -10000;\r
+      int index = 0;\r
+\r
+\r
+      do\r
+      {\r
+        Atom tmp = (Atom) maxChain.atoms.elementAt(index);\r
+        if (resNum != tmp.resNumber && tmp.alignmentMapping != -1)\r
+        {\r
+          resNum = tmp.resNumber;\r
+          mapping[tmp.alignmentMapping+1][0] = tmp.resNumber;\r
+          mapping[tmp.alignmentMapping+1][1] = tmp.atomIndex;\r
+        }\r
+\r
+        index++;\r
+      }\r
+      while(index < maxChain.atoms.size());\r
+\r
+      if (mappings == null)\r
+      {\r
+        mappings = new StructureMapping[1];\r
+      }\r
+      else\r
+      {\r
+        StructureMapping[] tmp = new StructureMapping[mappings.length + 1];\r
+        System.arraycopy(mappings, 0, tmp, 0, mappings.length);\r
+        mappings = tmp;\r
+      }\r
+\r
+      if(protocol.equals(jalview.io.AppletFormatAdapter.PASTE))\r
+        pdbFile = "INLINE"+pdb.id;\r
+\r
+      mappings[mappings.length - 1]\r
+          = new StructureMapping(sequence[s], pdbFile, pdb.id, maxChainId,\r
+                                 mapping, mappingDetails.toString());\r
+    }\r
+    /////////\r
+\r
+    return pdb;\r
+  }\r
+\r
+  public void removeStructureViewerListener(Object svl, String pdbfile)\r
+  {\r
+    listeners.removeElement(svl);\r
+\r
+    boolean removeMapping = true;\r
+\r
+    StructureListener sl;\r
+    for (int i = 0; i < listeners.size(); i++)\r
+    {\r
+      if (listeners.elementAt(i) instanceof StructureListener)\r
+      {\r
+        sl = (StructureListener) listeners.elementAt(i);\r
+        if (sl.getPdbFile().equals(pdbfile))\r
+        {\r
+          removeMapping = false;\r
+          break;\r
+        }\r
+      }\r
+    }\r
+\r
+    if (removeMapping && mappings!=null)\r
+    {\r
+      Vector tmp = new Vector();\r
+      for (int i = 0; i < mappings.length; i++)\r
+      {\r
+        if (!mappings[i].pdbfile.equals(pdbfile))\r
+        {\r
+          tmp.addElement(mappings[i]);\r
+        }\r
+      }\r
+\r
+      mappings = new StructureMapping[tmp.size()];\r
+      tmp.copyInto(mappings);\r
+    }\r
+  }\r
+\r
+  public void mouseOverStructure(int pdbResNum, String chain, String pdbfile)\r
+  {\r
+    SequenceListener sl;\r
+    for (int i = 0; i < listeners.size(); i++)\r
+    {\r
+      if (listeners.elementAt(i) instanceof SequenceListener)\r
+      {\r
+        sl = (SequenceListener) listeners.elementAt(i);\r
+\r
+        for (int j = 0; j < mappings.length; j++)\r
+        {\r
+          if (mappings[j].pdbfile.equals(pdbfile) &&\r
+              mappings[j].pdbchain.equals(chain))\r
+          {\r
+            sl.highlightSequence(mappings[j].sequence,\r
+                                 mappings[j].getSeqPos(pdbResNum));\r
+          }\r
+        }\r
+\r
+        sl.highlightSequence(null, pdbResNum);\r
+      }\r
+    }\r
+  }\r
+\r
+  public void mouseOverSequence(SequenceI seq, int index)\r
+  {\r
+    StructureListener sl;\r
+    int atomNo = 0;\r
+    for (int i = 0; i < listeners.size(); i++)\r
+    {\r
+      if (listeners.elementAt(i) instanceof StructureListener)\r
+      {\r
+        sl = (StructureListener) listeners.elementAt(i);\r
+\r
+        for (int j = 0; j < mappings.length; j++)\r
+        {\r
+          if (mappings[j].sequence == seq)\r
+          {\r
+            atomNo = mappings[j].getAtomNum(index);\r
+\r
+            if (atomNo > 0)\r
+            {\r
+              sl.highlightAtom(atomNo,\r
+                               mappings[j].getPDBResNum(index),\r
+                               mappings[j].pdbchain,\r
+                               mappings[j].pdbfile);\r
+            }\r
+          }\r
+        }\r
+      }\r
+    }\r
+  }\r
+\r
+  public void structureSelectionChanged()\r
+  {\r
+    StructureListener svl;\r
+    for (int i = 0; i < listeners.size(); i++)\r
+    {\r
+      svl = (StructureListener) listeners.elementAt(i);\r
+    }\r
+  }\r
+\r
+  public void sequenceSelectionChanged()\r
+  {\r
+    StructureListener svl;\r
+    for (int i = 0; i < listeners.size(); i++)\r
+    {\r
+      svl = (StructureListener) listeners.elementAt(i);\r
+    }\r
+  }\r
+\r
+  public void sequenceColoursChanged(Object source)\r
+  {\r
+    StructureListener sl;\r
+    for (int i = 0; i < listeners.size(); i++)\r
+    {\r
+      if (listeners.elementAt(i) instanceof StructureListener)\r
+      {\r
+        sl = (StructureListener) listeners.elementAt(i);\r
+        sl.updateColours(source);\r
+      }\r
+    }\r
+  }\r
+\r
+  public StructureMapping[] getMapping(String pdbfile)\r
+  {\r
+    Vector tmp = new Vector();\r
+    for (int i = 0; i < mappings.length; i++)\r
+    {\r
+      if (mappings[i].pdbfile.equals(pdbfile))\r
+      {\r
+        tmp.addElement(mappings[i]);\r
+      }\r
+    }\r
+\r
+    StructureMapping[] ret = new StructureMapping[tmp.size()];\r
+    for (int i = 0; i < tmp.size(); i++)\r
+    {\r
+      ret[i] = (StructureMapping) tmp.elementAt(i);\r
+    }\r
+\r
+    return ret;\r
+  }\r
+\r
+  public String printMapping(String pdbfile)\r
+  {\r
+    StringBuffer sb = new StringBuffer();\r
+    for (int i = 0; i < mappings.length; i++)\r
+    {\r
+      if (mappings[i].pdbfile.equals(pdbfile))\r
+      {\r
+        sb.append(mappings[i].mappingDetails);\r
+      }\r
+    }\r
+\r
+    return sb.toString();\r
+  }\r
+}\r