X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FStructureFrequency.java;h=08bb3fdd18dd0d9530bbdd8f172393718c74363f;hb=e498cc04385671872ab98220219aaeac2ec245f2;hp=67d8b9b481b4819df8d865b7878095060fc323d6;hpb=d20c94407cbb4122fdce7768d3d67dbf5ada50c6;p=jalview.git diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java index 67d8b9b..08bb3fd 100644 --- a/src/jalview/analysis/StructureFrequency.java +++ b/src/jalview/analysis/StructureFrequency.java @@ -1,21 +1,22 @@ /* - * 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) + * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 . */ + package jalview.analysis; import java.util.*; @@ -27,7 +28,7 @@ import jalview.datamodel.*; * 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 $Revision$ */ @@ -49,7 +50,7 @@ public class StructureFrequency /** * Returns the 3' position of a base pair - * + * * @param pairs * Secondary structure annotation * @param indice @@ -71,7 +72,7 @@ public class StructureFrequency /** * 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 @@ -123,41 +124,41 @@ public class StructureFrequency 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 @@ -214,7 +215,7 @@ public class StructureFrequency /** * Method to check if a base-pair is a canonical or a wobble bp - * + * * @param up * 5' base * @param down @@ -286,7 +287,7 @@ public class StructureFrequency /** * Compute all or part of the annotation row from the given consensus * hashtable - * + * * @param consensus * - pre-allocated annotation row * @param hconsensus @@ -311,7 +312,7 @@ public class StructureFrequency 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 @@ -322,32 +323,28 @@ public class StructureFrequency 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 @@ -355,8 +352,10 @@ public class StructureFrequency { 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 += @@ -405,7 +404,7 @@ public class StructureFrequency /** * get the sorted base-pair profile for the given position of the consensus - * + * * @param hconsensus * @return profile of the given column */ @@ -446,7 +445,7 @@ public class StructureFrequency 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]++]; } }