X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=13f928c977b7f1ef50232630a6c90ae5b4dca744;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=76704523bdb63ab4eb50cb3e2bf8f9ac96a3ea9d;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java index 7670452..13f928c 100755 --- a/src/jalview/datamodel/Sequence.java +++ b/src/jalview/datamodel/Sequence.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 2.6) + * 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.datamodel; @@ -62,14 +61,14 @@ public class Sequence implements SequenceI * Creates a new Sequence object. * * @param name - * display name string + * display name string * @param sequence - * string to form a possibly gapped sequence out of + * string to form a possibly gapped sequence out of * @param start - * first position of non-gap residue in the sequence + * first position of non-gap residue in the sequence * @param end - * last position of ungapped residues (nearly always only used - * for display purposes) + * last position of ungapped residues (nearly always only used for + * display purposes) */ public Sequence(String name, String sequence, int start, int end) { @@ -141,9 +140,9 @@ public class Sequence implements SequenceI * Creates a new Sequence object. * * @param name - * DOCUMENT ME! + * DOCUMENT ME! * @param sequence - * DOCUMENT ME! + * DOCUMENT ME! */ public Sequence(String name, String sequence) { @@ -156,7 +155,7 @@ public class Sequence implements SequenceI * reference. * * @param seq - * DOCUMENT ME! + * DOCUMENT ME! */ public Sequence(SequenceI seq) { @@ -169,9 +168,9 @@ public class Sequence implements SequenceI * annotation that is present in the given annotation array. * * @param seq - * the sequence to be copied + * the sequence to be copied * @param alAnnotation - * an array of annotation including some associated with seq + * an array of annotation including some associated with seq */ public Sequence(SequenceI seq, AlignmentAnnotation[] alAnnotation) { @@ -235,7 +234,7 @@ public class Sequence implements SequenceI * DOCUMENT ME! * * @param v - * DOCUMENT ME! + * DOCUMENT ME! */ public void setSequenceFeatures(SequenceFeature[] features) { @@ -331,7 +330,7 @@ public class Sequence implements SequenceI * DOCUMENT ME! * * @param id - * DOCUMENT ME! + * DOCUMENT ME! */ public void setPDBId(Vector id) { @@ -368,7 +367,7 @@ public class Sequence implements SequenceI * DOCUMENT ME! * * @param name - * DOCUMENT ME! + * DOCUMENT ME! */ public void setName(String name) { @@ -390,7 +389,7 @@ public class Sequence implements SequenceI * DOCUMENT ME! * * @param start - * DOCUMENT ME! + * DOCUMENT ME! */ public void setStart(int start) { @@ -411,7 +410,7 @@ public class Sequence implements SequenceI * DOCUMENT ME! * * @param end - * DOCUMENT ME! + * DOCUMENT ME! */ public void setEnd(int end) { @@ -442,7 +441,7 @@ public class Sequence implements SequenceI * DOCUMENT ME! * * @param seq - * DOCUMENT ME! + * DOCUMENT ME! */ public void setSequence(String seq) { @@ -497,9 +496,9 @@ public class Sequence implements SequenceI * seqeunce * * @param start - * int + * int * @param end - * int + * int * @return SequenceI */ public SequenceI getSubSequence(int start, int end) @@ -533,7 +532,7 @@ public class Sequence implements SequenceI * DOCUMENT ME! * * @param i - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -553,7 +552,7 @@ public class Sequence implements SequenceI * DOCUMENT ME! * * @param desc - * DOCUMENT ME! + * DOCUMENT ME! */ public void setDescription(String desc) { @@ -574,7 +573,7 @@ public class Sequence implements SequenceI * Return the alignment position for a sequence position * * @param pos - * lying from start to end + * lying from start to end * * @return aligned position of residue pos */ @@ -608,7 +607,7 @@ public class Sequence implements SequenceI * Returns the sequence position for an alignment position * * @param i - * column index in alignment (from 1) + * column index in alignment (from 1) * * @return residue number for residue (left of and) nearest ith column */ @@ -765,11 +764,11 @@ public class Sequence implements SequenceI * DOCUMENT ME! * * @param i - * DOCUMENT ME! + * DOCUMENT ME! * @param c - * DOCUMENT ME! + * DOCUMENT ME! * @param chop - * DOCUMENT ME! + * DOCUMENT ME! */ public void insertCharAt(int i, int length, char c) { @@ -991,8 +990,9 @@ public class Sequence implements SequenceI /* * (non-Javadoc) * - * @see jalview.datamodel.SequenceI#setAlignmentAnnotation(AlignmmentAnnotation[] - * annotations) + * @see + * jalview.datamodel.SequenceI#setAlignmentAnnotation(AlignmmentAnnotation[] + * annotations) */ public void setAlignmentAnnotation(AlignmentAnnotation[] annotations) { @@ -1103,8 +1103,9 @@ public class Sequence implements SequenceI /* * (non-Javadoc) * - * @see jalview.datamodel.SequenceI#transferAnnotation(jalview.datamodel.SequenceI, - * jalview.datamodel.Mapping) + * @see + * jalview.datamodel.SequenceI#transferAnnotation(jalview.datamodel.SequenceI, + * jalview.datamodel.Mapping) */ public void transferAnnotation(SequenceI entry, Mapping mp) {