/*
* 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/>.
*/
* 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 $Revision$
*/
/**
* Returns the 3' position of a base pair
- *
+ *
* @param pairs
* Secondary structure annotation
* @param indice
/**
* 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
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;
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
}
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);
- int[][] pairs = (int[][]) hconsensus[i]
+ int[][] pairs = (int[][]) hci
.get(StructureFrequency.PAIRPROFILE);
if (pairs != null && includeAllConsSymbols) // Just responsible for the
mouseOver = "";
/* 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 +=
{
ca[x] = new int[]
{ c, d };
- vl[x] = (float) pairs[c][d];
+ vl[x] = pairs[c][d];
x++;
}
}
{
if (vl[c] > 0)
{
- tval = ((float) vl[c] * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
+ tval = (vl[c] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1
: 0]);
mouseOver += ((p == 0) ? "" : "; ") + (char) ((int[]) ca[c])[0]
+ (char) ((int[]) ca[c])[1] + " " + ((int) tval) + "%";
/**
* 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[] rtnval = new int[52]; // 2*(5*5)+2
+ int[] rtnval = new int[74]; // 2*(5*5)+2
int[][] profile = (int[][]) hconsensus.get(StructureFrequency.PROFILE);
int[][] pairs = (int[][]) hconsensus
.get(StructureFrequency.PAIRPROFILE);
{
ca[x] = new int[]
{ c, d };
- vl[x] = (float) pairs[c][d];
+ vl[x] = pairs[c][d];
x++;
}
}
{
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]++];
}
git://source.jalview.org / jalview.git / blobdiff