Mapping for alignment added to residue

diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index 6ae2baa..51c4f01 100755 (executable)
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -32,6 +32,7 @@ public class Atom {
     int type;\r
     Color color;\r
     String chain;\r
+    int alignmentMapping=-1;\r
 \r
     public boolean isSelected = false;\r
 \r

diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java
index b3eb23f..4672271 100755 (executable)
--- a/src/MCview/PDBCanvas.java
+++ b/src/MCview/PDBCanvas.java
@@ -88,7 +88,7 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
         int pdbend = 0;\r
         int seqstart = 0;\r
         int seqend = 0;\r
-        int [] mapping = null;\r
+        AlignSeq maxAlignseq = null;;\r
 \r
         for (int i = 0; i < pdb.chains.size(); i++)\r
         {\r
@@ -126,7 +126,7 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
                 pdbend = as.seq2end;\r
                 seqstart = as.seq1start + sequence.getStart()-1;\r
                 seqend = as.seq1end + sequence.getEnd()-1;\r
-                mapping = as.getExactMapping();\r
+                maxAlignseq = as;\r
             }\r
 \r
             mappingDetails.append("\nPDB start/end "  + pdbstart + " " + pdbend);\r
@@ -140,7 +140,8 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
         mainchain.seqstart = seqstart;\r
         mainchain.seqend = seqend;\r
         mainchain.isVisible = true;\r
-        mainchain.seqMapping = mapping;\r
+        mainchain.makeExactMapping(maxAlignseq, sequence);\r
+\r
       //  mainchain.sequence = sequence;\r
 \r
       this.pdb = pdb;\r
@@ -182,15 +183,6 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
           }\r
        });\r
 \r
-      /*\r
-       SequenceGroup sg = new SequenceGroup("PDB",\r
-                                            null, true,true,false,\r
-                                            sequence.findIndex(seqstart-1),\r
-                                            sequence.findIndex(seqend-1));\r
-       sg.addSequence(sequence, false);\r
-       sg.setOutlineColour(Color.black);\r
-       seqcanvas.getViewport().getAlignment().addGroup(sg);\r
-       */\r
 \r
         findCentre();\r
         findWidth();\r
@@ -206,6 +198,7 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
         ToolTipManager.sharedInstance().setDismissDelay(10000);\r
     }\r
 \r
+\r
     Vector visiblebonds;\r
     void setupBonds()\r
     {\r
@@ -463,6 +456,35 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
       repaint();\r
     }\r
 \r
+    int findTrueIndex(int pos)\r
+    {\r
+      // returns the alignment position for a residue\r
+      int j = sequence.getStart();\r
+      int i = 0;\r
+\r
+      while ( (i < sequence.getLength()) && (j <= sequence.getEnd()) && (j <= pos+1))\r
+      {\r
+        if (!jalview.util.Comparison.isGap(sequence.getCharAt(i)))\r
+        {\r
+          j++;\r
+        }\r
+\r
+        i++;\r
+      }\r
+\r
+      if(i>1)\r
+         i--;\r
+\r
+      if ( (j == sequence.getEnd()) && (j < pos))\r
+      {\r
+        return sequence.getEnd() + 1;\r
+      }\r
+      else\r
+      {\r
+        return i;\r
+      }\r
+    }\r
+\r
     // This method has been taken out of PDBChain to allow\r
     // Applet and Application specific sequence renderers to be used\r
     void colourBySequence(PDBChain chain)\r
@@ -477,34 +499,30 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
         if ( (tmp.at1.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) &&\r
             (tmp.at1.resNumber <= ( (chain.offset + chain.pdbend) - 1)))\r
         {\r
-\r
-          int pos = // chain.seqstart + Don't include seqstart here, start from 0\r
-              (tmp.at1.resNumber - chain.pdbstart - chain.offset)+1;\r
-\r
-            int index = chain.seqMapping[pos];\r
+            int index = findTrueIndex(tmp.at1.alignmentMapping);\r
+                //sequence.findIndex(tmp.at1.alignmentMapping);\r
             if (index != -1)\r
             {\r
-              tmp.startCol = seqcanvas.getSequenceRenderer().findSequenceColour(\r
-                  Color.lightGray, sequence, index);\r
+              tmp.startCol = seqcanvas.getSequenceRenderer().\r
+                  getResidueBoxColour( sequence, index);\r
 \r
-              tmp.startCol = seqcanvas.getFeatureRenderer().findFeatureColour(tmp.\r
-                  startCol, sequence, index);\r
+              tmp.startCol = seqcanvas.getFeatureRenderer().\r
+                  findFeatureColour(tmp.startCol, sequence, index);\r
             }\r
         }\r
 \r
         if ( (tmp.at2.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) &&\r
             (tmp.at2.resNumber <= ( (chain.pdbend + chain.offset) - 1)))\r
         {\r
-          int pos = // chain.seqstart + Don't include seqstart here, start from 0\r
-              (tmp.at2.resNumber - chain.pdbstart - chain.offset)+1;\r
 \r
-            int index = chain.seqMapping[pos];\r
+            int index =  findTrueIndex(tmp.at2.alignmentMapping);\r
+                //sequence.findIndex( tmp.at2.alignmentMapping );\r
             if (index != -1)\r
             {\r
-              tmp.endCol = seqcanvas.getSequenceRenderer().findSequenceColour(\r
-                  tmp.endCol, sequence, index);\r
-              tmp.endCol = seqcanvas.getFeatureRenderer().findFeatureColour(tmp.\r
-                  endCol, sequence, index);\r
+              tmp.endCol = seqcanvas.getSequenceRenderer().\r
+                  getResidueBoxColour( sequence, index);\r
+              tmp.endCol = seqcanvas.getFeatureRenderer().\r
+                  findFeatureColour(tmp.endCol, sequence, index);\r
             }\r
         }\r
       }\r
@@ -652,18 +670,15 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
             PDBChain chain = (PDBChain) pdb.chains.elementAt(foundchain);\r
             if (chain == mainchain)\r
             {\r
-              int pos = // chain.seqstart + Don't include seqstart here, start from 0\r
-                  (fatom.resNumber - chain.pdbstart - chain.offset) +1 ;\r
-\r
-              if (chain.seqMapping[pos] != -1)\r
+              if (fatom.alignmentMapping != -1)\r
               {\r
                 if (highlightRes == null)\r
                   highlightRes = new Vector();\r
 \r
-                if (highlightRes.contains((chain.seqMapping[pos]) + ""))\r
-                  highlightRes.remove((chain.seqMapping[pos]) + "");\r
+                if (highlightRes.contains(fatom.alignmentMapping+"" + ""))\r
+                  highlightRes.remove(fatom.alignmentMapping + "");\r
                 else\r
-                  highlightRes.add((chain.seqMapping[pos]) + "");\r
+                  highlightRes.add(fatom.alignmentMapping + "");\r
               }\r
             }\r
           }\r
@@ -695,10 +710,7 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
           chain = (PDBChain) pdb.chains.elementAt(foundchain);\r
           if(chain == mainchain)\r
           {\r
-           int pos = // chain.seqstart + Don't include seqstart here, start from 0\r
-               (fatom.resNumber - chain.pdbstart - chain.offset) +1 ;\r
-\r
-            highlightSeqcanvas( chain.seqMapping[pos] );\r
+            highlightSeqcanvas( fatom.alignmentMapping );\r
           }\r
         }\r
 \r
@@ -928,42 +940,41 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
    public void highlightRes(int ii)\r
   {\r
 \r
-    int index = ii - mainchain.seqstart;\r
-\r
-    if (highlightRes!=null\r
-        && highlightRes.contains( mainchain.seqMapping[index]+ ""))\r
+    if (highlightRes != null\r
+        && highlightRes.contains((ii-1) + ""))\r
     {\r
-       return;\r
+      return;\r
     }\r
 \r
-    if(highlightBond1!=null)\r
-      highlightBond1.at2.isSelected = false;\r
-\r
-    if(highlightBond2!=null)\r
-      highlightBond2.at1.isSelected = false;\r
-\r
-    highlightBond1 = null;\r
-    highlightBond2 = null;\r
+    int index = -1;\r
+    Bond tmpBond;\r
+    for(index=0; index<mainchain.bonds.size(); index++)\r
+    {\r
+      tmpBond = (Bond) mainchain.bonds.elementAt(index);\r
+      if (tmpBond.at1.alignmentMapping == ii - 1)\r
+      {\r
+        if (highlightBond1 != null)\r
+          highlightBond1.at2.isSelected = false;\r
 \r
+        if (highlightBond2 != null)\r
+          highlightBond2.at1.isSelected = false;\r
 \r
+        highlightBond1 = null;\r
+        highlightBond2 = null;\r
 \r
-    if(index <0 )\r
-      return;\r
+        if (index > 0)\r
+        {\r
+          highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1);\r
+          highlightBond1.at2.isSelected = true;\r
+        }\r
 \r
-    if(index<=mainchain.bonds.size())\r
-    {\r
-      if(index>0)\r
-      {\r
-        highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1);\r
-        highlightBond1.at2.isSelected = true;\r
-       // highlightBond1.at2.isSelected = true;\r
-      }\r
+        if (index != mainchain.bonds.size())\r
+        {\r
+          highlightBond2 = (Bond) mainchain.bonds.elementAt(index);\r
+          highlightBond2.at1.isSelected = true;\r
+        }\r
 \r
-      if(index!=mainchain.bonds.size())\r
-      {\r
-        highlightBond2 = (Bond) mainchain.bonds.elementAt(index);\r
-        highlightBond2.at1.isSelected = true;\r
-     //   highlightBond2.at2.isSelected = true;\r
+        break;\r
       }\r
     }\r
 \r

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 3cf73d1..276525b 100755 (executable)
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -25,6 +25,7 @@ import jalview.schemes.ResidueProperties;
 import java.awt.*;\r
 \r
 import java.util.*;\r
+import jalview.analysis.AlignSeq;\r
 \r
 \r
 public class PDBChain {\r
@@ -39,7 +40,6 @@ public class PDBChain {
     public int pdbend = 0;\r
     public int seqstart = 0;\r
     public int seqend = 0;\r
-    public int [] seqMapping;\r
 \r
     //public DrawableSequence ds;\r
     public PDBChain(String id) {\r
@@ -58,6 +58,38 @@ public class PDBChain {
         return tmp;\r
     }\r
 \r
+    void makeExactMapping(AlignSeq as, Sequence s1)\r
+    {\r
+        int pdbpos =   as.getSeq2Start()-2;\r
+        int alignpos = s1.getStart() + as.getSeq1Start()-3;\r
+\r
+        for(int i=0; i<as.astr1.length(); i++)\r
+        {\r
+            if (as.astr1.charAt(i) != '-')\r
+            {\r
+              alignpos++;\r
+            }\r
+\r
+            if (as.astr2.charAt(i) != '-')\r
+            {\r
+              pdbpos++;\r
+            }\r
+\r
+            if (as.astr1.charAt(i) == as.astr2.charAt(i))\r
+            {\r
+                Residue res = (Residue) residues.elementAt(pdbpos);\r
+                Enumeration en = res.atoms.elements();\r
+                while (en.hasMoreElements())\r
+                {\r
+                  Atom atom = (Atom) en.nextElement();\r
+                  atom.alignmentMapping = alignpos;\r
+                }\r
+            }\r
+        }\r
+\r
+    }\r
+\r
+\r
     public void makeCaBondList()\r
     {\r
         for (int i = 0; i < (residues.size() - 1); i++)\r