/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
* 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
+ * 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
+ *
+ * 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/>.
*/
+
package jalview.analysis;
import java.util.*;
* returns a new Hashtable[] of size maxSeqLength, if Hashtable not supplied.
* This class is used extensively in calculating alignment colourschemes that
* depend on the amount of conservation in each alignment column.
- *
+ *
* @author $author$
* @version $Revision$
*/
public static final String PAIRPROFILE = "B";
-/**
- * Returns the 3' position of a base pair
- * @param pairs Secondary structure annotation
- * @param indice 5' position of a base pair
- * @return 3' position of a base pair
- */
+ /**
+ * Returns the 3' position of a base pair
+ *
+ * @param pairs
+ * Secondary structure annotation
+ * @param indice
+ * 5' position of a base pair
+ * @return 3' position of a base pair
+ */
public static int findPair(SequenceFeature[] pairs, int indice)
{
for (int i = 0; i < pairs.length; i++)
/**
* Method to calculate a 'base pair consensus row', very similar to nucleotide
* consensus but takes into account a given structure
- *
+ *
* @param sequences
* @param start
* @param end
values = new int[255];
pairs = new int[255][255];
bpEnd = -1;
- if(i<struc.length){
+ if (i < struc.length)
+ {
s = struc[i];
- }else{
+ }
+ else
+ {
s = '-';
}
if (s == '.' || s == ' ')
}
else
{
+ bpEnd = findPair(rna, i);
+ if (bpEnd>-1)
+ {
for (j = 0; j < jSize; j++) // foreach row
{
if (sequences[j] == null)
.println("WARNING: Consensus skipping null sequence - possible race condition.");
continue;
}
- seq = sequences[j].getSequence();
-
- if (seq.length > i)
+ c = sequences[j].getCharAt(i);
{
- c = seq[i];
// standard representation for gaps in sequence and structure
if (c == '.' || c == ' ')
values['-']++;
continue;
}
- bpEnd = findPair(rna, i);
- cEnd = seq[bpEnd];
+ cEnd = sequences[j].getCharAt(bpEnd);
if (checkBpType(c, cEnd))
{
values['(']++; // H means it's a helix (structured)
maxResidue = "(";
}
}
+ }
// nonGap++;
}
// UPDATE this for new values
residueHash.put(MAXCOUNT, new Integer(count));
residueHash.put(MAXRESIDUE, maxResidue);
- percentage = ((float) count * 100) / (float) jSize;
+ percentage = ((float) count * 100) / jSize;
residueHash.put(PID_GAPS, new Float(percentage));
// percentage = ((float) count * 100) / (float) nongap;
result[i] = residueHash;
}
if (bpEnd > 0)
- {
- values[')']=values['('];
- values['(']=0;
-
+ {
+ values[')'] = values['('];
+ values['('] = 0;
+
residueHash = new Hashtable();
maxResidue = ")";
-
+
if (profile)
{
residueHash.put(PROFILE, new int[][]
residueHash.put(PAIRPROFILE, pairs);
}
-
+
residueHash.put(MAXCOUNT, new Integer(count));
residueHash.put(MAXRESIDUE, maxResidue);
- percentage = ((float) count * 100) / (float) jSize;
+ percentage = ((float) count * 100) / jSize;
residueHash.put(PID_GAPS, new Float(percentage));
-
result[bpEnd] = residueHash;
}
}
/**
* Method to check if a base-pair is a canonical or a wobble bp
- *
+ *
* @param up
* 5' base
* @param down
/**
* Compute all or part of the annotation row from the given consensus
* hashtable
- *
+ *
* @param consensus
* - pre-allocated annotation row
* @param hconsensus
boolean ignoreGapsInConsensusCalculation,
boolean includeAllConsSymbols)
{
- completeConsensus(consensus, hconsensus, iStart, width,
- ignoreGapsInConsensusCalculation, includeAllConsSymbols, null); // new
- // char[]
- // { 'A', 'C', 'G', 'T', 'U' });
- }
-
- public static void completeConsensus(AlignmentAnnotation consensus,
- Hashtable[] hconsensus, int iStart, int width,
- boolean ignoreGapsInConsensusCalculation,
- boolean includeAllConsSymbols, char[] alphabet)
- {
float tval, value;
if (consensus == null || consensus.annotations == null
|| consensus.annotations.length < width)
}
for (int i = iStart; i < width; i++)
{
- if (i >= hconsensus.length)
+ Hashtable hci;
+ if (i >= hconsensus.length || ((hci=hconsensus[i])==null))
{
// happens if sequences calculated over were shorter than alignment
// width
continue;
}
value = 0;
+ Float fv;
if (ignoreGapsInConsensusCalculation)
{
- value = ((Float) hconsensus[i].get(StructureFrequency.PID_NOGAPS))
- .floatValue();
+ fv =(Float) hci.get(StructureFrequency.PID_NOGAPS);
}
else
{
- value = ((Float) hconsensus[i].get(StructureFrequency.PID_GAPS))
- .floatValue();
+ fv = (Float) hci.get(StructureFrequency.PID_GAPS);
}
-
- String maxRes = hconsensus[i].get(StructureFrequency.MAXRESIDUE)
+ if (fv==null)
+ {
+ consensus.annotations[i] = null;
+ // data has changed below us .. give up and
+ continue;
+ }
+ value = fv.floatValue();
+ String maxRes = hci.get(StructureFrequency.MAXRESIDUE)
.toString();
- String mouseOver = hconsensus[i].get(StructureFrequency.MAXRESIDUE)
+ String mouseOver = hci.get(StructureFrequency.MAXRESIDUE)
+ " ";
if (maxRes.length() > 1)
{
mouseOver = "[" + maxRes + "] ";
maxRes = "+";
}
- int[][] profile = (int[][]) hconsensus[i]
+ int[][] profile = (int[][]) hci
.get(StructureFrequency.PROFILE);
- if (profile != null && includeAllConsSymbols) // Just responsible for the
+ int[][] pairs = (int[][]) hci
+ .get(StructureFrequency.PAIRPROFILE);
+
+ if (pairs != null && includeAllConsSymbols) // Just responsible for the
// tooltip
- //TODO Update tooltips for Structure row
+ // TODO Update tooltips for Structure row
{
mouseOver = "";
- if (alphabet != null)
+
+ /* TODO It's not sure what is the purpose of the alphabet and wheter it is useful for structure?
+ *
+ * if (alphabet != null) { for (int c = 0; c < alphabet.length; c++) {
+ * tval = ((float) profile[0][alphabet[c]]) 100f / (float)
+ * profile[1][ignoreGapsInConsensusCalculation ? 1 : 0]; mouseOver +=
+ * ((c == 0) ? "" : "; ") + alphabet[c] + " " + ((int) tval) + "%"; } }
+ * else {
+ */
+ Object[] ca = new Object[625];
+ float[] vl = new float[625];
+ int x = 0;
+ for (int c = 65; c < 90; c++)
{
- for (int c = 0; c < alphabet.length; c++)
+ for (int d = 65; d < 90; d++)
{
- tval = ((float) profile[0][alphabet[c]])
- * 100f
- / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
- : 0];
- mouseOver += ((c == 0) ? "" : "; ") + alphabet[c] + " "
- + ((int) tval) + "%";
+ ca[x] = new int[]
+ { c, d };
+ vl[x] = pairs[c][d];
+ x++;
}
}
- else
+ jalview.util.QuickSort.sort(vl, ca);
+ int p = 0;
+
+ for (int c = 624; c > 0; c--)
{
- Object[] ca = new Object[profile[0].length];
- float[] vl = new float[profile[0].length];
- for (int c = 0; c < ca.length; c++)
+ if (vl[c] > 0)
{
- ca[c] = new char[]
- { (char) c };
- vl[c] = (float) profile[0][c];
- }
- ;
- jalview.util.QuickSort.sort(vl, ca);
- for (int p = 0, c = ca.length - 1; profile[0][((char[]) ca[c])[0]] > 0; c--)
- {
- if (((char[]) ca[c])[0] != '-')
- {
- tval = ((float) profile[0][((char[]) ca[c])[0]])
- * 100f
- / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
- : 0];
- mouseOver += ((p == 0) ? "" : "; ") + ((char[]) ca[c])[0]
- + " " + ((int) tval) + "%";
- p++;
+ tval = (vl[c] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1
+ : 0]);
+ mouseOver += ((p == 0) ? "" : "; ") + (char) ((int[]) ca[c])[0]
+ + (char) ((int[]) ca[c])[1] + " " + ((int) tval) + "%";
+ p++;
- }
}
-
}
+
+ // }
}
else
{
/**
* get the sorted base-pair profile for the given position of the consensus
- *
+ *
* @param hconsensus
* @return profile of the given column
*/
public static int[] extractProfile(Hashtable hconsensus,
- boolean ignoreGapsInConsensusCalculation, int column)
+ boolean ignoreGapsInConsensusCalculation)
{
- // TODO is there a more elegant way to acces the column number?
- /*
- * calculate the frequence of the 16 bp variations for this column 'somehow'
- * transfer this via getProfile and let it correctly draw
- */
- int[] rtnval = new int[51]; // 2*(5*5)+1
+ int[] rtnval = new int[74]; // 2*(5*5)+2
int[][] profile = (int[][]) hconsensus.get(StructureFrequency.PROFILE);
int[][] pairs = (int[][]) hconsensus
.get(StructureFrequency.PAIRPROFILE);
if (profile == null)
return null;
-
+
+ // TODO fix the object length, also do it in completeConsensus
Object[] ca = new Object[625];
float[] vl = new float[625];
- int x=0;
+ int x = 0;
for (int c = 65; c < 90; c++)
{
- for(int d = 65; d< 90; d++)
+ for (int d = 65; d < 90; d++)
{
- ca[x] = new int[]{ c, d};
- vl[x] = (float) pairs[c][d];
- x++;
+ ca[x] = new int[]
+ { c, d };
+ vl[x] = pairs[c][d];
+ x++;
}
}
jalview.util.QuickSort.sort(vl, ca);
-
- rtnval[0] = 1;
- for (int c=624; c>0; c--)
+
+ rtnval[0] = 2;
+ rtnval[1] = 0;
+ for (int c = 624; c > 0; c--)
{
- if (vl[c]>0)
+ if (vl[c] > 0)
{
rtnval[rtnval[0]++] = ((int[]) ca[c])[0];
rtnval[rtnval[0]++] = ((int[]) ca[c])[1];
- rtnval[rtnval[0]++] = (int) ((float) vl[c] * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
+ rtnval[rtnval[0]] = (int) (vl[c] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1
: 0]);
- }
+ rtnval[1]+=rtnval[rtnval[0]++];
+ }
}
-
+
return rtnval;
}
git://source.jalview.org / jalview.git / blobdiff