/*
- * 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
- *
+ * 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
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-
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 $Revision$
*/
/**
* 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
else
{
bpEnd = findPair(rna, i);
- if (bpEnd>-1)
- {
- for (j = 0; j < jSize; j++) // foreach row
+ if (bpEnd > -1)
{
- if (sequences[j] == null)
- {
- System.err
- .println("WARNING: Consensus skipping null sequence - possible race condition.");
- continue;
- }
- c = sequences[j].getCharAt(i);
+ for (j = 0; j < jSize; j++) // foreach row
{
-
- // standard representation for gaps in sequence and structure
- if (c == '.' || c == ' ')
+ if (sequences[j] == null)
{
- c = '-';
- }
-
- if (c == '-')
- {
- values['-']++;
+ System.err
+ .println("WARNING: Consensus skipping null sequence - possible race condition.");
continue;
}
- cEnd = sequences[j].getCharAt(bpEnd);
- if (checkBpType(c, cEnd))
+ c = sequences[j].getCharAt(i);
{
- values['(']++; // H means it's a helix (structured)
- }
- pairs[c][cEnd]++;
- maxResidue = "(";
+ // standard representation for gaps in sequence and structure
+ if (c == '.' || c == ' ')
+ {
+ c = '-';
+ }
+
+ if (c == '-')
+ {
+ values['-']++;
+ continue;
+ }
+ cEnd = sequences[j].getCharAt(bpEnd);
+ if (checkBpType(c, cEnd))
+ {
+ values['(']++; // H means it's a helix (structured)
+ }
+ pairs[c][cEnd]++;
+
+ maxResidue = "(";
+ }
}
}
- }
// nonGap++;
}
// UPDATE this for new values
/**
* 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++)
{
Hashtable hci;
- if (i >= hconsensus.length || ((hci=hconsensus[i])==null))
+ if (i >= hconsensus.length || ((hci = hconsensus[i]) == null))
{
// happens if sequences calculated over were shorter than alignment
// width
Float fv;
if (ignoreGapsInConsensusCalculation)
{
- fv =(Float) hci.get(StructureFrequency.PID_NOGAPS);
+ fv = (Float) hci.get(StructureFrequency.PID_NOGAPS);
}
else
{
fv = (Float) hci.get(StructureFrequency.PID_GAPS);
}
- if (fv==null)
+ 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 = hci.get(StructureFrequency.MAXRESIDUE)
- + " ";
+ String maxRes = hci.get(StructureFrequency.MAXRESIDUE).toString();
+ String mouseOver = hci.get(StructureFrequency.MAXRESIDUE) + " ";
if (maxRes.length() > 1)
{
mouseOver = "[" + maxRes + "] ";
maxRes = "+";
}
- int[][] profile = (int[][]) hci
- .get(StructureFrequency.PROFILE);
- int[][] pairs = (int[][]) hci
- .get(StructureFrequency.PAIRPROFILE);
+ int[][] profile = (int[][]) hci.get(StructureFrequency.PROFILE);
+ int[][] pairs = (int[][]) hci.get(StructureFrequency.PAIRPROFILE);
if (pairs != null && includeAllConsSymbols) // Just responsible for the
// tooltip
{
mouseOver = "";
- /* TODO It's not sure what is the purpose of the alphabet and wheter it is useful for structure?
- *
+ /*
+ * 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 +=
/**
* get the sorted base-pair profile for the given position of the consensus
- *
+ *
* @param hconsensus
* @return profile of the given column
*/
rtnval[rtnval[0]++] = ((int[]) ca[c])[1];
rtnval[rtnval[0]] = (int) (vl[c] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1
: 0]);
- rtnval[1]+=rtnval[rtnval[0]++];
+ rtnval[1] += rtnval[rtnval[0]++];
}
}
git://source.jalview.org / jalview.git / blobdiff