X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBChain.java;h=669a7e8e2ecd81afc08f5746123c894ef13add54;hb=6486a5333807ca300db4a28a6bf9899f5dddf5a6;hp=61ad26a2cbdc32e8281792039d3ee46d3aceeb0d;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git
diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 61ad26a..669a7e8 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -1,20 +1,19 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * 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 General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
*/
package MCview;
@@ -47,7 +46,7 @@ public class PDBChain
public int offset;
public Sequence sequence;
-
+ public boolean isNa=false;
public boolean isVisible = true;
public int pdbstart = 0;
@@ -116,7 +115,7 @@ public class PDBChain
*
* @param seq
* @param status
- * The Status of the transferred annotation
+ * The Status of the transferred annotation
* @return the features added to sq (or its dataset)
*/
public SequenceFeature[] transferRESNUMFeatures(SequenceI seq,
@@ -134,8 +133,8 @@ public class PDBChain
/**
* Remove any existing features for this chain if they exist ?
* SequenceFeature[] seqsfeatures=seq.getSequenceFeatures(); int
- * totfeat=seqsfeatures.length; // Remove any features for this exact chain ?
- * for (int i=0; i0 && ((numNa/residues.size())>0.99))
+ {
+ isNa=true;
+ }
}
public void makeBond(Atom at1, Atom at2)
@@ -204,6 +219,8 @@ public class PDBChain
public void makeResidueList()
{
int count = 0;
+ Object symbol;
+ boolean nucleotide = false;
StringBuffer seq = new StringBuffer();
Vector resFeatures = new Vector();
Vector resAnnotation = new Vector();
@@ -254,17 +271,30 @@ public class PDBChain
resFeatures.addElement(sf);
resAnnotation.addElement(new Annotation(tmpat.tfactor));
// Keep totting up the sequence
- if (ResidueProperties.getAA3Hash().get(tmpat.resName) == null)
+ if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null)
{
- seq.append("X");
- // System.err.println("PDBReader:Null aa3Hash for " +
- // tmpat.resName);
+ String nucname=tmpat.resName.trim();
+ if (ResidueProperties.nucleotideIndex[nucname.charAt(0)] == -1)
+ {
+ seq.append("X");
+ // System.err.println("PDBReader:Null aa3Hash for " +
+ // tmpat.resName);
+ }
+ else
+ {
+ // nucleotide flag
+ nucleotide = true;
+ seq.append(nucname.charAt(0));
+ }
}
else
{
-
- seq.append(ResidueProperties.aa[((Integer) ResidueProperties
- .getAA3Hash().get(tmpat.resName)).intValue()]);
+ if (nucleotide)
+ {
+ System.err
+ .println("Warning: mixed nucleotide and amino acid chain.. its gonna do bad things to you!");
+ }
+ seq.append(ResidueProperties.aa[((Integer) symbol).intValue()]);
}
count++;
}
@@ -273,15 +303,14 @@ public class PDBChain
{
id = " ";
}
-
+ isNa=nucleotide;
sequence = new Sequence(id, seq.toString(), offset, resNumber - 1); // Note:
- // resNumber-offset
- // ~=
- // seq.size()
+ // resNumber-offset
+ // ~=
+ // seq.size()
// Add normalised feature scores to RESNUM indicating start/end of sequence
- // sf.setScore(offset+count);
-
-
+ // sf.setScore(offset+count);
+
// System.out.println("PDB Sequence is :\nSequence = " + seq);
// System.out.println("No of residues = " + residues.size());
for (i = 0, iSize = resFeatures.size(); i < iSize; i++)
@@ -300,7 +329,7 @@ public class PDBChain
resAnnotation.setElementAt(null, i);
}
AlignmentAnnotation tfactorann = new AlignmentAnnotation(
- "PDB.CATempFactor", "CA Temperature Factor for "
+ "PDB.TempFactor", "Temperature Factor for "
+ sequence.getName(), annots, 0, max,
AlignmentAnnotation.LINE_GRAPH);
tfactorann.setSequenceRef(sequence);