X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=aded6e8faae93b48031aa0c6fcd7d903fdd17186;hb=abeb1ce92e146611f2e7b57ff3e0f8169a216991;hp=10bee55bf5be6e3d3833a4378ee97e3768c2e397;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java index 10bee55..aded6e8 100755 --- a/src/jalview/datamodel/SequenceI.java +++ b/src/jalview/datamodel/SequenceI.java @@ -1,24 +1,23 @@ /* - * 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 2.8) + * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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. + * + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ package jalview.datamodel; -import java.util.*; +import java.util.Vector; /** * DOCUMENT ME! @@ -44,7 +43,7 @@ public interface SequenceI * Set start position of first non-gapped symbol in sequence * * @param start - * new start position + * new start position */ public void setStart(int start); @@ -88,7 +87,7 @@ public interface SequenceI * Replace the sequence with the given string * * @param sequence - * new sequence string + * new sequence string */ public void setSequence(String sequence); @@ -101,9 +100,9 @@ public interface SequenceI * get a range on the seuqence as a string * * @param start - * DOCUMENT ME! + * DOCUMENT ME! * @param end - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -120,9 +119,9 @@ public interface SequenceI * get stretch of sequence characters in an array * * @param start - * absolute index into getSequence() + * absolute index into getSequence() * @param end - * exclusive index of last position in segment to be returned. + * exclusive index of last position in segment to be returned. * * @return char[max(0,end-start)]; */ @@ -132,9 +131,9 @@ public interface SequenceI * create a new sequence object from start to end of this sequence * * @param start - * int + * int * @param end - * int + * int * @return SequenceI */ public SequenceI getSubSequence(int start, int end); @@ -143,7 +142,7 @@ public interface SequenceI * DOCUMENT ME! * * @param i - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -153,7 +152,7 @@ public interface SequenceI * DOCUMENT ME! * * @param desc - * DOCUMENT ME! + * DOCUMENT ME! */ public void setDescription(String desc); @@ -165,12 +164,18 @@ public interface SequenceI public String getDescription(); /** - * DOCUMENT ME! + * Return the alignment column for a sequence position * Return the alignment + * position for a sequence position * * @param pos - * DOCUMENT ME! + * lying from start to end + * + * @return aligned column for residue (0 if residue is upstream from + * alignment, -1 if residue is downstream from alignment) note. + * Sequence object returns sequence.getEnd() for positions upstream + * currently. TODO: change sequence for + * assert(findIndex(seq.getEnd()+1)==-1) and fix incremental bugs * - * @return DOCUMENT ME! */ public int findIndex(int pos); @@ -178,7 +183,7 @@ public interface 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 */ @@ -207,9 +212,9 @@ public interface SequenceI * if necessary and adjusting start and end positions accordingly. * * @param i - * first column in range to delete + * first column in range to delete * @param j - * last column in range to delete + * last column in range to delete */ public void deleteChars(int i, int j); @@ -217,9 +222,9 @@ public interface SequenceI * DOCUMENT ME! * * @param i - * DOCUMENT ME! + * DOCUMENT ME! * @param c - * DOCUMENT ME! + * DOCUMENT ME! */ public void insertCharAt(int i, char c); @@ -227,9 +232,9 @@ public interface SequenceI * DOCUMENT ME! * * @param i - * DOCUMENT ME! + * DOCUMENT ME! * @param c - * DOCUMENT ME! + * DOCUMENT ME! */ public void insertCharAt(int i, int length, char c); @@ -244,7 +249,7 @@ public interface SequenceI * DOCUMENT ME! * * @param v - * DOCUMENT ME! + * DOCUMENT ME! */ public void setSequenceFeatures(SequenceFeature[] features); @@ -252,7 +257,7 @@ public interface SequenceI * DOCUMENT ME! * * @param id - * DOCUMENT ME! + * DOCUMENT ME! */ public void setPDBId(Vector ids); @@ -326,7 +331,7 @@ public interface SequenceI * Get one or more alignment annotations with a particular label. * * @param label - * string which each returned annotation must have as a label. + * string which each returned annotation must have as a label. * @return null or array of annotations. */ public AlignmentAnnotation[] getAnnotation(String label); @@ -346,8 +351,19 @@ public interface SequenceI * * @param entry * @param mp - * null or mapping from entry's numbering to local start/end + * null or mapping from entry's numbering to local start/end */ public void transferAnnotation(SequenceI entry, Mapping mp); + /** + * @param index + * The sequence index in the MSA + */ + public void setIndex(int index); + + /** + * @return The index of the sequence in the alignment + */ + public int getIndex(); + }