X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FRangetype.java;h=64a07e13fa80a89b935ed822a498e39bfa281761;hb=67b3acb8df1438ef37a756c04e14f5a3b8406808;hp=fb16f5548c8c5758e0db835c898d6262eced1d0c;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git diff --git a/src/jalview/io/vamsas/Rangetype.java b/src/jalview/io/vamsas/Rangetype.java index fb16f55..64a07e1 100644 --- a/src/jalview/io/vamsas/Rangetype.java +++ b/src/jalview/io/vamsas/Rangetype.java @@ -1,23 +1,31 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1) - * Copyright (C) 2014 The Jalview Authors + * 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.MapList; +import jalview.util.MessageManager; + +import java.util.List; import java.util.Vector; import uk.ac.vamsas.client.Vobject; @@ -26,7 +34,6 @@ 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.io.VamsasAppDatastore; /** * Enhances DatastoreItem objects with additional functions to do with RangeType @@ -73,8 +80,7 @@ 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) { @@ -132,8 +138,7 @@ 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) { @@ -180,8 +185,7 @@ 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) { @@ -221,15 +225,15 @@ 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); } @@ -244,26 +248,26 @@ public abstract class Rangetype extends DatastoreItem * @param default unit for mapped * @return MapList */ - protected jalview.util.MapList parsemapType(MapType maprange, int localu, + protected MapList parsemapType(MapType maprange, int localu, int mappedu) { - jalview.util.MapList ml = null; + MapList ml = null; int[] localRange = getIntervals(maprange.getLocal()); int[] mappedRange = getIntervals(maprange.getMapped()); long lu = maprange.getLocal().hasUnit() ? maprange.getLocal().getUnit() : localu; long mu = maprange.getMapped().hasUnit() ? maprange.getMapped() .getUnit() : mappedu; - ml = new jalview.util.MapList(localRange, mappedRange, (int) lu, + ml = new MapList(localRange, mappedRange, (int) lu, (int) mu); return ml; } - protected jalview.util.MapList parsemapType(MapType map) + protected MapList parsemapType(MapType map) { if (!map.getLocal().hasUnit() || map.getMapped().hasUnit()) { - jalview.bin.Cache.log + Cache.log .warn("using default mapping length of 1:1 for map " + (map.isRegistered() ? map.getVorbaId().toString() : (" " + map.toString()))); @@ -278,7 +282,7 @@ public abstract class Rangetype extends DatastoreItem * @param ml * @param setUnits */ - protected void initMapType(MapType maprange, jalview.util.MapList ml, + protected void initMapType(MapType maprange, MapList ml, boolean setUnits) { initMapType(maprange, ml, setUnits, false); @@ -292,13 +296,12 @@ public abstract class Rangetype extends DatastoreItem * @param reverse * - reverse MapList mapping for Local and Mapped ranges and units */ - protected void initMapType(MapType maprange, jalview.util.MapList ml, + protected void initMapType(MapType maprange, MapList ml, boolean setUnits, boolean reverse) { if (ml == null) { - throw new Error( - "Implementation error. MapList is null for initMapType."); + throw new Error(MessageManager.getString("error.implementation_error_maplist_is_null")); } maprange.setLocal(new Local()); maprange.setMapped(new Mapped());