X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FRangetype.java;h=786a46b86949e21181e932acf37bf3217386a076;hb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;hp=c4b817d1bbc759f171032ed237f02fa3437e3ddc;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git diff --git a/src/jalview/io/vamsas/Rangetype.java b/src/jalview/io/vamsas/Rangetype.java index c4b817d..786a46b 100644 --- a/src/jalview/io/vamsas/Rangetype.java +++ b/src/jalview/io/vamsas/Rangetype.java @@ -1,34 +1,38 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * 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 - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * + * 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 Jalview. If not, see . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.io.vamsas; +import jalview.bin.Cache; +import jalview.io.VamsasAppDatastore; +import jalview.util.MessageManager; + +import java.util.List; import java.util.Vector; import uk.ac.vamsas.client.Vobject; import uk.ac.vamsas.objects.core.Local; -import uk.ac.vamsas.objects.core.Map; import uk.ac.vamsas.objects.core.MapType; import uk.ac.vamsas.objects.core.Mapped; import uk.ac.vamsas.objects.core.RangeType; import uk.ac.vamsas.objects.core.Seg; -import jalview.datamodel.DBRefEntry; -import jalview.datamodel.Mapping; -import jalview.io.VamsasAppDatastore; /** * Enhances DatastoreItem objects with additional functions to do with RangeType @@ -50,7 +54,8 @@ public abstract class Rangetype extends DatastoreItem super(datastore); } - public Rangetype(VamsasAppDatastore datastore, Vobject vobj, Class jvClass) + public Rangetype(VamsasAppDatastore datastore, Vobject vobj, + Class jvClass) { super(datastore, vobj, jvClass); } @@ -75,8 +80,8 @@ public abstract class Rangetype extends DatastoreItem int[] se = null; if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0) { - throw new Error( - "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!"); + throw new Error(MessageManager.getString( + "error.invalid_vamsas_rangetype_cannot_resolve_lists")); } if (dseta.getSegCount() > 0) { @@ -99,8 +104,7 @@ public abstract class Rangetype extends DatastoreItem // could do a polarity for pos range too. and pass back indication of // discontinuities. int pos = dseta.getPos(0).getI(); - se = new int[] - { pos, pos }; + se = new int[] { pos, pos }; for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++) { pos = dseta.getPos(p).getI(); @@ -134,8 +138,8 @@ public abstract class Rangetype extends DatastoreItem int[] se = null; if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0) { - throw new Error( - "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!"); + throw new Error(MessageManager.getString( + "error.invalid_vamsas_rangetype_cannot_resolve_lists")); } if (dseta.getSegCount() > 0) { @@ -145,7 +149,7 @@ public abstract class Rangetype extends DatastoreItem int se_end = se[1 - se[2]] + (se[2] == 0 ? 1 : -1); for (int p = se[se[2]]; p != se_end; p += se[2] == 0 ? 1 : -1) { - posList.add(new Integer(p)); + posList.add(Integer.valueOf(p)); } } } @@ -156,7 +160,7 @@ public abstract class Rangetype extends DatastoreItem for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++) { pos = dseta.getPos(p).getI(); - posList.add(new Integer(pos)); + posList.add(Integer.valueOf(pos)); } } } @@ -182,16 +186,16 @@ public abstract class Rangetype extends DatastoreItem int[] se = null; if (range.getSegCount() > 0 && range.getPosCount() > 0) { - throw new Error( - "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!"); + throw new Error(MessageManager.getString( + "error.invalid_vamsas_rangetype_cannot_resolve_lists")); } if (range.getSegCount() > 0) { for (int s = 0, sSize = range.getSegCount(); s < sSize; s++) { se = getSegRange(range.getSeg(s), false); - posList.addElement(new Integer(se[0])); - posList.addElement(new Integer(se[1])); + posList.addElement(Integer.valueOf(se[0])); + posList.addElement(Integer.valueOf(se[1])); } } else if (range.getPosCount() > 0) @@ -201,8 +205,8 @@ public abstract class Rangetype extends DatastoreItem for (int p = 0, pSize = range.getPosCount(); p < pSize; p++) { pos = range.getPos(p).getI(); - posList.add(new Integer(pos)); - posList.add(new Integer(pos)); + posList.add(Integer.valueOf(pos)); + posList.add(Integer.valueOf(pos)); } } } @@ -223,15 +227,15 @@ public abstract class Rangetype extends DatastoreItem * initialise a range type object from a set of start/end inclusive intervals * * @param mrt - * @param range + * @param ranges */ - protected void initRangeType(RangeType mrt, int[] range) + protected void initRangeType(RangeType mrt, List ranges) { - for (int i = 0; i < range.length; i += 2) + for (int[] range : ranges) { Seg vSeg = new Seg(); - vSeg.setStart(range[i]); - vSeg.setEnd(range[i + 1]); + vSeg.setStart(range[0]); + vSeg.setEnd(range[1]); vSeg.setInclusive(true); mrt.addSeg(vSeg); } @@ -242,8 +246,10 @@ public abstract class Rangetype extends DatastoreItem * @param maprange * where the from range is the local mapped range, and the to range * is the 'mapped' range in the MapRangeType - * @param default unit for local - * @param default unit for mapped + * @param default + * unit for local + * @param default + * unit for mapped * @return MapList */ protected jalview.util.MapList parsemapType(MapType maprange, int localu, @@ -254,8 +260,9 @@ public abstract class Rangetype extends DatastoreItem int[] mappedRange = getIntervals(maprange.getMapped()); long lu = maprange.getLocal().hasUnit() ? maprange.getLocal().getUnit() : localu; - long mu = maprange.getMapped().hasUnit() ? maprange.getMapped() - .getUnit() : mappedu; + long mu = maprange.getMapped().hasUnit() + ? maprange.getMapped().getUnit() + : mappedu; ml = new jalview.util.MapList(localRange, mappedRange, (int) lu, (int) mu); return ml; @@ -265,8 +272,7 @@ public abstract class Rangetype extends DatastoreItem { if (!map.getLocal().hasUnit() || map.getMapped().hasUnit()) { - jalview.bin.Cache.log - .warn("using default mapping length of 1:1 for map " + Cache.warn("using default mapping length of 1:1 for map " + (map.isRegistered() ? map.getVorbaId().toString() : (" " + map.toString()))); }