X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FStructureFrequency.java;h=42e8847fb301940d3c88188fc0c7ec9748b0d38b;hb=3385d3fe7b3acd45dc5aaa3c7d73f7cce5ea7457;hp=7b97a8dd3691a4ac179dfaf4ae0a180360dccad3;hpb=7b7397a32734f990b14ea0a3bf49d3a9e1d928c3;p=jalview.git diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java index 7b97a8d..42e8847 100644 --- a/src/jalview/analysis/StructureFrequency.java +++ b/src/jalview/analysis/StructureFrequency.java @@ -46,12 +46,15 @@ public class StructureFrequency 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++) @@ -96,9 +99,12 @@ public class StructureFrequency values = new int[255]; pairs = new int[255][255]; bpEnd = -1; - if(i 0) - { - values[')']=values['(']; - values['(']=0; - + { + values[')'] = values['(']; + values['('] = 0; + residueHash = new Hashtable(); maxResidue = ")"; - + if (profile) { residueHash.put(PROFILE, new int[][] @@ -193,14 +199,13 @@ public class StructureFrequency residueHash.put(PAIRPROFILE, pairs); } - + residueHash.put(MAXCOUNT, new Integer(count)); residueHash.put(MAXRESIDUE, maxResidue); percentage = ((float) count * 100) / (float) jSize; residueHash.put(PID_GAPS, new Float(percentage)); - result[bpEnd] = residueHash; } } @@ -294,17 +299,6 @@ public class StructureFrequency 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) @@ -345,51 +339,53 @@ public class StructureFrequency } int[][] profile = (int[][]) hconsensus[i] .get(StructureFrequency.PROFILE); - if (profile != null && includeAllConsSymbols) // Just responsible for the + int[][] pairs = (int[][]) hconsensus[i] + .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] = (float) 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++) - { - 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 (vl[c] > 0) { - 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 = ((float) vl[c] * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1 + : 0]); + mouseOver += ((p == 0) ? "" : "; ") + (char) ((int[]) ca[c])[0] + + (char) ((int[]) ca[c])[1] + " " + ((int) tval) + "%"; + p++; - } } - } + + // } } else { @@ -407,13 +403,8 @@ public class StructureFrequency * @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[][] profile = (int[][]) hconsensus.get(StructureFrequency.PROFILE); int[][] pairs = (int[][]) hconsensus @@ -421,33 +412,35 @@ public class StructureFrequency 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] = (float) pairs[c][d]; + x++; } } jalview.util.QuickSort.sort(vl, ca); - + rtnval[0] = 1; - for (int c=624; c>0; c--) + 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 : 0]); - } + } } - + return rtnval; }