X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueProperties.java;h=8acf1f2a40ce029a83e24200d4f2360a88af3766;hb=2273eba5668e5340354da60fed329c6c716cc439;hp=301a410d5f2bb394433ecad649f9e031f11be4d5;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git
diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 301a410..8acf1f2 100755
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -6,14 +6,16 @@
*
* 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.
+ * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
@@ -21,13 +23,17 @@ package jalview.schemes;
import jalview.analysis.scoremodels.PIDScoreModel;
import jalview.api.analysis.ScoreModelI;
-import java.util.*;
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.Hashtable;
import java.util.List;
-import java.awt.*;
+import java.util.Map;
+import java.util.Vector;
public class ResidueProperties
{
- public static Hashtable scoreMatrices = new Hashtable();
+ public static Hashtable scoreMatrices = new Hashtable();
// Stores residue codes/names and colours and other things
public static final int[] aaIndex; // aaHash version 2.1.1 and below
@@ -695,19 +701,20 @@ public class ResidueProperties
}
/**
- * Nucleotide Ambiguity Codes
+ * Nucleotide Ambiguity Codes
*/
- public static final Hashtable ambiguityCodes=new Hashtable();
+ public static final Hashtable ambiguityCodes = new Hashtable();
+
/**
- * Codon triplets with additional symbols for unambiguous codons that include ambiguity codes
+ * Codon triplets with additional symbols for unambiguous codons that include
+ * ambiguity codes
*/
- public static final Hashtable codonHash2 = new Hashtable();
-
+ public static final Hashtable codonHash2 = new Hashtable();
+
/**
* all ambiguity codes for a given base
*/
- public final static Hashtable> _ambiguityCodes = new Hashtable>();
-
+ public final static Hashtable> _ambiguityCodes = new Hashtable>();
static
{
@@ -892,10 +899,10 @@ public class ResidueProperties
codonHash2.put("TTC", "F");
codonHash2.put("TTT", "F");
-
+
buildAmbiguityCodonSet();
}
-
+
/**
* programmatic generation of codons including ambiguity codes
*/
@@ -931,7 +938,8 @@ public class ResidueProperties
}
// and programmatically add in the ambiguity codes that yield the same amino
// acid
- String[] unambcodons = codonHash2.keySet().toArray(new String[codonHash2.size()]);
+ String[] unambcodons = codonHash2.keySet().toArray(
+ new String[codonHash2.size()]);
for (String codon : unambcodons)
{
String residue = codonHash2.get(codon);
@@ -966,7 +974,7 @@ public class ResidueProperties
char _anuc;
for (ipos = 0; ipos < tpos.length; ipos++)
{
- if (acodon[ipos].length==0 || tpos[ipos] < 0)
+ if (acodon[ipos].length == 0 || tpos[ipos] < 0)
{
_acodon += codon.charAt(ipos);
allres[ipos] = new char[]
@@ -998,7 +1006,7 @@ public class ResidueProperties
_codon += allres[j][cpos[j]];
}
String tr = codonHash2.get(_codon);
- if (valid = (tr!=null && tr.equals(residue)))
+ if (valid = (tr != null && tr.equals(residue)))
{
// advance to next combination
ipos = acodon.length - 1;
@@ -1012,14 +1020,14 @@ public class ResidueProperties
if (valid)
{
// Add this to the set of codons we will translate
-// System.out.println("Adding ambiguity codon: " + _acodon + " for "
-// + residue);
+ // System.out.println("Adding ambiguity codon: " + _acodon + " for "
+ // + residue);
codonHash2.put(_acodon, residue);
}
else
{
-// System.err.println("Rejecting ambiguity codon: " + _acodon
-// + " for " + residue);
+ // System.err.println("Rejecting ambiguity codon: " + _acodon
+ // + " for " + residue);
}
// next combination
ipos = acodon.length - 1;
@@ -1420,62 +1428,75 @@ public class ResidueProperties
}
static
{
- int[][] propMatrixF = new int[maxProteinIndex][maxProteinIndex],
- propMatrixPos = new int[maxProteinIndex][maxProteinIndex],
- propMatrixEpos = new int[maxProteinIndex][maxProteinIndex];
- for (int i=0;ii) {
- ic+=aa[i];
+ int maxF = 0, maxP = 0, maxEP = 0;
+ String ic = "";
+ if (aa.length > i)
+ {
+ ic += aa[i];
+ }
+ else
+ {
+ ic = "-";
}
- else {ic = "-";}
- for (int j=i+1;jj) {
- jc+=aa[j];
+ String jc = "";
+ if (aa.length > j)
+ {
+ jc += aa[j];
}
- else {jc = "-";}
- propMatrixF[i][j]=0;
- propMatrixPos[i][j]=0;
- propMatrixEpos[i][j]=0;
- for (Enumeration en= (Enumeration)propHash.keys(); en.hasMoreElements(); )
+ else
+ {
+ jc = "-";
+ }
+ propMatrixF[i][j] = 0;
+ propMatrixPos[i][j] = 0;
+ propMatrixEpos[i][j] = 0;
+ for (Enumeration en = propHash.keys(); en
+ .hasMoreElements();)
{
String ph = en.nextElement();
- Map pph=(Map)propHash.get(ph);
- if (pph.get(ic)!=null && pph.get(jc)!=null) {
- int icp=pph.get(ic).intValue(),jcp=pph.get(jc).intValue();
+ Map pph = (Map) propHash
+ .get(ph);
+ if (pph.get(ic) != null && pph.get(jc) != null)
+ {
+ int icp = pph.get(ic).intValue(), jcp = pph.get(jc).intValue();
// Still working on these definitions.
- propMatrixPos[i][j] += icp == jcp && icp>0 ? 2 : 0;
- propMatrixPos[j][i] += icp == jcp && icp>0 ? 2 : 0;
+ propMatrixPos[i][j] += icp == jcp && icp > 0 ? 2 : 0;
+ propMatrixPos[j][i] += icp == jcp && icp > 0 ? 2 : 0;
propMatrixF[i][j] += icp == jcp ? 2 : 0;
propMatrixF[j][i] += icp == jcp ? 2 : 0;
- propMatrixEpos[i][j] += icp == jcp ? (1+icp * 2) : 0;
- propMatrixEpos[j][i] += icp == jcp ? (1+icp * 2) : 0;
- }}
- if (maxF toRNAssState;
+
+ public static boolean RNAcloseParen[] = new boolean[255];
static
{
- toRNAssState = new Hashtable();
+ toRNAssState = new Hashtable();
toRNAssState.put(")", "(");
toRNAssState.put("(", "(");
toRNAssState.put("]", "[");
@@ -1740,7 +1765,15 @@ public class ResidueProperties
toRNAssState.put("y", "Y");
toRNAssState.put("Z", "Z");
toRNAssState.put("z", "Z");
-
+ for (int p = 0; p < RNAcloseParen.length; p++)
+ {
+ RNAcloseParen[p] = false;
+ }
+ for (String k : toRNAssState.keySet())
+ {
+ RNAcloseParen[k.charAt(0)] = k.charAt(0) != toRNAssState.get(k)
+ .charAt(0);
+ }
}
/**
@@ -1761,7 +1794,8 @@ public class ResidueProperties
String ssc = ssstring.substring(i, i + 1);
if (toRNAssState.containsKey(ssc))
{
- ss.append((String) toRNAssState.get(ssc));
+ // valid ss character - so return it
+ ss.append(ssc); // (String) toRNAssState.get(ssc));
}
else
{
@@ -1771,6 +1805,11 @@ public class ResidueProperties
return ss.toString();
}
+ public static boolean isCloseParenRNA(char dc)
+ {
+ return RNAcloseParen[dc];
+ }
+
// main method generates perl representation of residue property hash
// / cut here
public static void main(String[] args)
@@ -1820,4 +1859,5 @@ public class ResidueProperties
System.out.println("};");
}
// to here
+
}