X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=15727ef31efa3ea88f74bc25ca3466abcfb85074;hb=d423f22792e47dbc800ae220a58677f988971d06;hp=c9ae0446605b4fa6ed1ac598379c789d6c76aed2;hpb=797d4400e51c5786c080d7d746d5968589b5dc78;p=jalview.git diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java index c9ae044..15727ef 100755 --- a/src/jalview/analysis/AlignSeq.java +++ b/src/jalview/analysis/AlignSeq.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) + * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * This program 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. + * Jalview is free software: you can redistribute it and/or + * 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. * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * 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; @@ -113,17 +112,17 @@ public class AlignSeq String type; - private int[] charToInt; + private int[] charToInt; /** * Creates a new AlignSeq object. * * @param s1 - * DOCUMENT ME! + * DOCUMENT ME! * @param s2 - * DOCUMENT ME! + * DOCUMENT ME! * @param type - * DOCUMENT ME! + * DOCUMENT ME! */ public AlignSeq(SequenceI s1, SequenceI s2, String type) { @@ -135,11 +134,11 @@ public class AlignSeq * Creates a new AlignSeq object. * * @param s1 - * DOCUMENT ME! + * DOCUMENT ME! * @param s2 - * DOCUMENT ME! + * DOCUMENT ME! * @param type - * DOCUMENT ME! + * DOCUMENT ME! */ public AlignSeq(SequenceI s1, String string1, SequenceI s2, String string2, String type) @@ -271,15 +270,15 @@ public class AlignSeq * DOCUMENT ME! * * @param s1 - * DOCUMENT ME! - * @param string1 - - * string to align for sequence1 + * DOCUMENT ME! + * @param string1 + * - string to align for sequence1 * @param s2 - * sequence 2 - * @param string2 - - * string to align for sequence2 + * sequence 2 + * @param string2 + * - string to align for sequence2 * @param type - * DNA or PEPTIDE + * DNA or PEPTIDE */ public void SeqInit(SequenceI s1, String string1, SequenceI s2, String string2, String type) @@ -604,7 +603,7 @@ public class AlignSeq * DOCUMENT ME! * * @param mat - * DOCUMENT ME! + * DOCUMENT ME! */ public void printScoreMatrix(int[][] mat) { @@ -644,9 +643,9 @@ public class AlignSeq * DOCUMENT ME! * * @param i - * DOCUMENT ME! + * DOCUMENT ME! * @param j - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -718,7 +717,7 @@ public class AlignSeq { E[i][0] = -gapOpen; F[i][0] = max(score[i - 1][0] - gapOpen, F[i - 1][0] - gapExtend); - + score[i][0] = max(lookup[seq1[i]][seq2[0]] * 10, E[i][0], F[i][0]); traceback[i][0] = -1; } @@ -742,9 +741,9 @@ public class AlignSeq * DOCUMENT ME! * * @param gapChar - * DOCUMENT ME! + * DOCUMENT ME! * @param seq - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -765,11 +764,11 @@ public class AlignSeq * DOCUMENT ME! * * @param i1 - * DOCUMENT ME! + * DOCUMENT ME! * @param i2 - * DOCUMENT ME! + * DOCUMENT ME! * @param i3 - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -794,9 +793,9 @@ public class AlignSeq * DOCUMENT ME! * * @param i1 - * DOCUMENT ME! + * DOCUMENT ME! * @param i2 - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -816,9 +815,9 @@ public class AlignSeq * DOCUMENT ME! * * @param s - * DOCUMENT ME! + * DOCUMENT ME! * @param type - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -839,11 +838,12 @@ public class AlignSeq try { seq1[i] = charToInt[c]; // set accordingly from setType - if (seq1[i]<0 || seq1[i] > defInt) // set from setType: 23 for peptides, or 4 for NA. + if (seq1[i] < 0 || seq1[i] > defInt) // set from setType: 23 for + // peptides, or 4 for NA. { seq1[i] = defInt; } - + } catch (Exception e) { seq1[i] = defInt; @@ -857,15 +857,15 @@ public class AlignSeq * DOCUMENT ME! * * @param g - * DOCUMENT ME! + * DOCUMENT ME! * @param mat - * DOCUMENT ME! + * DOCUMENT ME! * @param n - * DOCUMENT ME! + * DOCUMENT ME! * @param m - * DOCUMENT ME! + * DOCUMENT ME! * @param psize - * DOCUMENT ME! + * DOCUMENT ME! */ public static void displayMatrix(Graphics g, int[][] mat, int n, int m, int psize)