New WSWUBlast Client files

[jalview.git] / src / MCview / PDBChain.java

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 166e537..43c8e9d 100755 (executable)
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -34,7 +34,7 @@ public class PDBChain {
     public Vector residues = new Vector();\r
     public int offset;\r
     public Sequence sequence;\r
-    public boolean isVisible = false;\r
+    public boolean isVisible = true;\r
     public int pdbstart = 0;\r
     public int pdbend = 0;\r
     public int seqstart = 0;\r
@@ -61,8 +61,8 @@ public class PDBChain {
         for (int i = 0; i < (residues.size() - 1); i++) {\r
             Residue tmpres = (Residue) residues.elementAt(i);\r
             Residue tmpres2 = (Residue) residues.elementAt(i + 1);\r
-            myAtom at1 = tmpres.findAtom("CA");\r
-            myAtom at2 = tmpres2.findAtom("CA");\r
+            Atom at1 = tmpres.findAtom("CA");\r
+            Atom at2 = tmpres2.findAtom("CA");\r
 \r
             if ((at1 != null) && (at2 != null)) {\r
                 if (at1.chain.equals(at2.chain)) {\r
@@ -72,7 +72,7 @@ public class PDBChain {
         }\r
     }\r
 \r
-    public void makeBond(myAtom at1, myAtom at2) {\r
+    public void makeBond(Atom at1, Atom at2) {\r
         float[] start = new float[3];\r
         float[] end = new float[3];\r
 \r
@@ -92,7 +92,7 @@ public class PDBChain {
         String seq = "";\r
 \r
         for (int i = 0; i < atoms.size(); i++) {\r
-            myAtom tmp = (myAtom) atoms.elementAt(i);\r
+            Atom tmp = (Atom) atoms.elementAt(i);\r
             //String resName = tmp.resName;\r
             int resNumber = tmp.resNumber;\r
             int res = resNumber;\r
@@ -103,18 +103,18 @@ public class PDBChain {
 \r
             Vector resAtoms = new Vector();\r
 \r
-            resAtoms.addElement((myAtom) atoms.elementAt(i));\r
+            resAtoms.addElement((Atom) atoms.elementAt(i));\r
             i++;\r
-            resNumber = ((myAtom) atoms.elementAt(i)).resNumber;\r
+            resNumber = ((Atom) atoms.elementAt(i)).resNumber;\r
 \r
             //Add atoms to a vector while the residue number\r
             //remains the same\r
             while ((resNumber == res) && (i < atoms.size())) {\r
-                resAtoms.addElement((myAtom) atoms.elementAt(i));\r
+                resAtoms.addElement((Atom) atoms.elementAt(i));\r
                 i++;\r
 \r
                 if (i < atoms.size()) {\r
-                    resNumber = ((myAtom) atoms.elementAt(i)).resNumber;\r
+                    resNumber = ((Atom) atoms.elementAt(i)).resNumber;\r
                 } else {\r
                     resNumber++;\r
                 }\r
@@ -128,7 +128,7 @@ public class PDBChain {
             count++;\r
 \r
             Residue tmpres = (Residue) residues.lastElement();\r
-            myAtom tmpat = (myAtom) tmpres.atoms.elementAt(0);\r
+            Atom tmpat = (Atom) tmpres.atoms.elementAt(0);\r
 \r
             // Keep totting up the sequence\r
             if (ResidueProperties.getAA3Hash().get(tmpat.resName) == null) {\r
@@ -139,12 +139,14 @@ public class PDBChain {
                                                                                   .get(tmpat.resName)).intValue()];\r
                 seq = seq + tmpres2;\r
             }\r
-\r
         }\r
 \r
-        sequence = new Sequence("PDB_seq", seq, 1, seq.length());\r
-      //  System.out.println("PDB Sequence is :\nSequence = " + seq);\r
-      //  System.out.println("No of residues = " + residues.size());\r
+        if(id.length()<1 || id.equals(" "))\r
+           id = "_";\r
+\r
+        sequence = new Sequence(id, seq, 1, seq.length());\r
+     //   System.out.println("PDB Sequence is :\nSequence = " + seq);\r
+     //   System.out.println("No of residues = " + residues.size());\r
     }\r
 \r
     public void setChargeColours() {\r
@@ -229,59 +231,15 @@ public class PDBChain {
         }\r
     }\r
 \r
-    public void colourBySequence(jalview.gui.SequenceRenderer sr,\r
-                                 jalview.gui.FeatureRenderer fr)\r
-    {\r
 \r
+\r
+    public void setChainColours(Color col)\r
+    {\r
         for (int i = 0; i < bonds.size(); i++)\r
         {\r
             Bond tmp = (Bond) bonds.elementAt(i);\r
-\r
-                if ((tmp.at1.resNumber >= ((offset + pdbstart) - 1)) &&\r
-                        (tmp.at1.resNumber <= ((offset + pdbend) - 1)))\r
-                    {\r
-                    int pos = seqstart +\r
-                        (tmp.at1.resNumber - pdbstart - offset);\r
-\r
-\r
-                    int index = sequence.findIndex(pos);\r
-\r
-                    tmp.startCol = sr.findSequenceColour(Color.gray, sequence,  index);\r
-\r
-                    tmp.startCol = fr.findFeatureColour(tmp.startCol, sequence, index);\r
-\r
-                } else\r
-                {\r
-                    tmp.startCol = Color.gray;\r
-                }\r
-\r
-                if ((tmp.at2.resNumber >= ((offset + pdbstart) - 1)) &&\r
-                        (tmp.at2.resNumber <= ((pdbend + offset) - 1))) {\r
-                    int pos = seqstart +\r
-                        (tmp.at2.resNumber - pdbstart - offset);\r
-                    int index = sequence.findIndex(pos);\r
-\r
-                   tmp.endCol = sr.findSequenceColour(Color.gray, sequence, index);\r
-                   tmp.endCol = fr.findFeatureColour( tmp.endCol, sequence, index);\r
-                }\r
-                else\r
-                {\r
-                    tmp.endCol = Color.gray;\r
-                }\r
-        }\r
-    }\r
-\r
-    public void setChainColours() {\r
-        for (int i = 0; i < bonds.size(); i++) {\r
-            Bond tmp = (Bond) bonds.elementAt(i);\r
-\r
-            try {\r
-                tmp.startCol = (Color) ResidueProperties.getChainColours().get(id);\r
-                tmp.endCol = (Color) ResidueProperties.getChainColours().get(id);\r
-            } catch (Exception e) {\r
-                tmp.startCol = Color.lightGray;\r
-                tmp.endCol = Color.lightGray;\r
-            }\r
+            tmp.startCol = col;\r
+            tmp.endCol = col;\r
         }\r
     }\r
 }\r