/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* 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.
- *
+ *
* 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package MCview;
public int offset;
public Sequence sequence;
- public boolean isNa=false;
+
+ public boolean isNa = false;
+
public boolean isVisible = true;
public int pdbstart = 0;
this.id = id;
}
+ /**
+ * character used to write newlines
+ */
+ protected String newline = System.getProperty("line.separator");
+
+ public void setNewlineString(String nl)
+ {
+ newline = nl;
+ }
+
+ public String getNewlineString()
+ {
+ return newline;
+ }
+
public String print()
{
String tmp = "";
{
tmp = tmp + ((Bond) bonds.elementAt(i)).at1.resName + " "
+ ((Bond) bonds.elementAt(i)).at1.resNumber + " " + offset
- + "\n";
+ + newline;
}
return tmp;
}
+ /**
+ * Annotate the residues with their corresponding positions in s1 using the
+ * alignment in as NOTE: This clears all atom.alignmentMapping values on the
+ * structure.
+ *
+ * @param as
+ * @param s1
+ */
public void makeExactMapping(AlignSeq as, SequenceI s1)
{
int pdbpos = as.getSeq2Start() - 2;
int alignpos = s1.getStart() + as.getSeq1Start() - 3;
-
+ // first clear out any old alignmentMapping values:
+ for (Atom atom : (Vector<Atom>) atoms)
+ {
+ atom.alignmentMapping = -1;
+ }
+ // and now trace the alignment onto the atom set.
for (int i = 0; i < as.astr1.length(); i++)
{
if (as.astr1.charAt(i) != '-')
- offset)).atoms.elementAt(0)).alignmentMapping);
tx.setEnd(1 + ((Atom) ((Residue) residues.elementAt(tx.getEnd()
- offset)).atoms.elementAt(0)).alignmentMapping);
- tx
- .setStatus(status
- + ((tx.getStatus() == null || tx.getStatus()
- .length() == 0) ? "" : ":" + tx.getStatus()));
+ tx.setStatus(status
+ + ((tx.getStatus() == null || tx.getStatus().length() == 0) ? ""
+ : ":" + tx.getStatus()));
if (tx.begin != 0 && tx.end != 0)
sq.addSequenceFeature(tx);
}
public void makeCaBondList()
{
- boolean na=false;
- int numNa=0;
+ boolean na = false;
+ int numNa = 0;
for (int i = 0; i < (residues.size() - 1); i++)
{
Residue tmpres = (Residue) residues.elementAt(i);
Residue tmpres2 = (Residue) residues.elementAt(i + 1);
Atom at1 = tmpres.findAtom("CA");
Atom at2 = tmpres2.findAtom("CA");
- na=false;
+ na = false;
if ((at1 == null) && (at2 == null))
{
- na=true;
+ na = true;
at1 = tmpres.findAtom("P");
at2 = tmpres2.findAtom("P");
}
System.out.println("not found " + i);
}
}
- if (numNa>0 && ((numNa/residues.size())>0.99))
+ if (numNa > 0 && ((numNa / residues.size()) > 0.99))
{
- isNa=true;
+ isNa = true;
}
}
{
int count = 0;
Object symbol;
+ boolean deoxyn = false;
boolean nucleotide = false;
StringBuffer seq = new StringBuffer();
Vector resFeatures = new Vector();
// Keep totting up the sequence
if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null)
{
- String nucname=tmpat.resName.trim();
- if (ResidueProperties.nucleotideIndex[nucname.charAt(0)] == -1)
+ String nucname = tmpat.resName.trim();
+ // use the aaIndex rather than call 'toLower' - which would take a bit
+ // more time.
+ deoxyn = nucname.length() == 2
+ && ResidueProperties.aaIndex[nucname.charAt(0)] == ResidueProperties.aaIndex['D'];
+ if (tmpat.name.equalsIgnoreCase("CA")
+ || ResidueProperties.nucleotideIndex[nucname
+ .charAt((deoxyn ? 1 : 0))] == -1)
{
seq.append("X");
// System.err.println("PDBReader:Null aa3Hash for " +
{
// nucleotide flag
nucleotide = true;
- seq.append(nucname.charAt(0));
+ seq.append(nucname.charAt((deoxyn ? 1 : 0)));
}
}
else
{
id = " ";
}
- isNa=nucleotide;
+ isNa = nucleotide;
sequence = new Sequence(id, seq.toString(), offset, resNumber - 1); // Note:
// resNumber-offset
// ~=
}
}
}
- sq
- .addAlignmentAnnotation(new AlignmentAnnotation("PDB.RESNUM",
- "PDB Residue Numbering for " + this.pdbid + ":"
- + this.id, an, (float) min, (float) max,
- AlignmentAnnotation.LINE_GRAPH));
+ sq.addAlignmentAnnotation(new AlignmentAnnotation("PDB.RESNUM",
+ "PDB Residue Numbering for " + this.pdbid + ":" + this.id,
+ an, (float) min, (float) max, AlignmentAnnotation.LINE_GRAPH));
}
}
}
git://source.jalview.org / jalview.git / blobdiff