// private key for ENA location designed not to conflict with real GFF data
private static final String LOCATION = "!Location";
+ private static final String ROW_DATA = "<tr><td>%s</td><td>%s</td></tr>";
+
+ /*
+ * map of otherDetails special keys, and their value fields' delimiter
+ */
+ private static final Map<String, String> INFO_KEYS = new HashMap<>();
+
+ static
+ {
+ INFO_KEYS.put("CSQ", ",");
++ // todo capture second level metadata (CSQ FORMAT)
++ // and delimiter "|" so as to report in a table within a table?
+ }
+
/*
* ATTRIBUTES is reserved for the GFF 'column 9' data, formatted as
* name1=value1;name2=value2,value3;...etc
{
return begin == 0 && end == 0;
}
+
+ /**
+ * Answers an html-formatted report of feature details
+ *
+ * @return
+ */
+ public String getDetailsReport()
+ {
+ StringBuilder sb = new StringBuilder(128);
+ sb.append("<br>");
+ sb.append("<table>");
+ sb.append(String.format(ROW_DATA, "Type", type));
+ sb.append(String.format(ROW_DATA, "Start/end", begin == end ? begin
+ : begin + (isContactFeature() ? ":" : "-") + end));
+ String desc = StringUtils.stripHtmlTags(description);
+ sb.append(String.format(ROW_DATA, "Description", desc));
+ if (!Float.isNaN(score) && score != 0f)
+ {
+ sb.append(String.format(ROW_DATA, "Score", score));
+ }
+ if (featureGroup != null)
+ {
+ sb.append(String.format(ROW_DATA, "Group", featureGroup));
+ }
+
+ if (otherDetails != null)
+ {
+ TreeMap<String, Object> ordered = new TreeMap<>(
+ String.CASE_INSENSITIVE_ORDER);
+ ordered.putAll(otherDetails);
+
+ for (Entry<String, Object> entry : ordered.entrySet())
+ {
+ String key = entry.getKey();
+ if (ATTRIBUTES.equals(key))
+ {
+ continue; // to avoid double reporting
+ }
- sb.append("<tr><td>").append(key).append("</td><td>");
+ if (INFO_KEYS.containsKey(key))
+ {
+ /*
+ * split selected INFO data by delimiter over multiple lines
+ */
- sb.append("</td></tr>");
+ String delimiter = INFO_KEYS.get(key);
+ String[] values = entry.getValue().toString().split(delimiter);
+ for (String value : values)
+ {
- sb.append("<tr><td> </td><td>").append(value)
++ sb.append("<tr><td>").append(key).append("</td><td>")
++ .append(value)
+ .append("</td></tr>");
+ }
+ }
+ else
- {
++ { // tried <td title="key"> but it failed to provide a tooltip :-(
++ sb.append("<tr><td>").append(key).append("</td><td>");
+ sb.append(entry.getValue().toString()).append("</td></tr>");
+ }
+ }
+ }
+ sb.append("</table>");
+
+ String text = sb.toString();
+ return text;
+ }
}
--- /dev/null
+ /*
+ * Copyright (c) 2011, 2012, Oracle and/or its affiliates. All rights reserved.
+ * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
+ *
+ * This code is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU General Public License version 2 only, as
+ * published by the Free Software Foundation. Oracle designates this
+ * particular file as subject to the "Classpath" exception as provided
+ * by Oracle in the LICENSE file that accompanied this code.
+ *
+ * This code 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
+ * version 2 for more details (a copy is included in the LICENSE file that
+ * accompanied this code).
+ *
+ * You should have received a copy of the GNU General Public License version
+ * 2 along with this work; if not, write to the Free Software Foundation,
+ * Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * Please contact Oracle, 500 Oracle Parkway, Redwood Shores, CA 94065 USA
+ * or visit www.oracle.com if you need additional information or have any
+ * questions.
+ */
+
+ package jalview.gui;
+
+ import java.awt.Container;
+ import java.beans.PropertyVetoException;
+ import java.util.Vector;
+
+ import javax.swing.DefaultDesktopManager;
+ import javax.swing.DesktopManager;
+ import javax.swing.JInternalFrame;
+
+ /**
+ * Based on AquaInternalFrameManager
+ *
+ * DesktopManager implementation for Aqua
+ *
+ * Mac is more like Windows than it's like Motif/Basic
+ *
+ * From WindowsDesktopManager:
+ *
+ * This class implements a DesktopManager which more closely follows the MDI
+ * model than the DefaultDesktopManager. Unlike the DefaultDesktopManager
+ * policy, MDI requires that the selected and activated child frames are the
+ * same, and that that frame always be the top-most window.
+ * <p>
+ * The maximized state is managed by the DesktopManager with MDI, instead of
+ * just being a property of the individual child frame. This means that if the
+ * currently selected window is maximized and another window is selected, that
+ * new window will be maximized.
+ *
+ * Downloaded from
+ * https://raw.githubusercontent.com/frohoff/jdk8u-jdk/master/src/macosx/classes/com/apple/laf/AquaInternalFrameManager.java
+ *
+ * Patch from Jim Procter - when the most recently opened frame is closed,
+ * correct behaviour is to go to the next most recent frame, rather than wrap
+ * around to the bottom of the window stack (as the original implementation
+ * does)
+ *
- * @see com.sun.java.swing.plaf.windows.WindowsDesktopManager
+ */
+ public class AquaInternalFrameManager extends DefaultDesktopManager
+ {
+ // Variables
+
+ /* The frame which is currently selected/activated.
+ * We store this value to enforce Mac's single-selection model.
+ */
+ JInternalFrame fCurrentFrame;
+
+ JInternalFrame fInitialFrame;
+
+ /* The list of frames, sorted by order of creation.
+ * This list is necessary because by default the order of
+ * child frames in the JDesktopPane changes during frame
+ * activation (the activated frame is moved to index 0).
+ * We preserve the creation order so that "next" and "previous"
+ * frame actions make sense.
+ */
+ Vector<JInternalFrame> fChildFrames = new Vector<>(1);
+
+ /**
+ * keep a reference to the original LAF manager so we can iconise/de-iconise
+ * correctly
+ */
+ private DesktopManager ourManager;
+
+ public AquaInternalFrameManager(DesktopManager desktopManager)
+ {
+ ourManager = desktopManager;
+ }
+
+ @Override
+ public void closeFrame(final JInternalFrame f)
+ {
+ if (f == fCurrentFrame)
+ {
+ boolean mostRecentFrame = fChildFrames
+ .indexOf(f) == fChildFrames.size() - 1;
+ if (!mostRecentFrame)
+ {
+ activateNextFrame();
+ }
+ else
+ {
+ activatePreviousFrame();
+ }
+ }
+ fChildFrames.removeElement(f);
+ super.closeFrame(f);
+ }
+
+ @Override
+ public void deiconifyFrame(final JInternalFrame f)
+ {
+ JInternalFrame.JDesktopIcon desktopIcon;
+
+ desktopIcon = f.getDesktopIcon();
+ // If the icon moved, move the frame to that spot before expanding it
+ // reshape does delta checks for us
+ f.reshape(desktopIcon.getX(), desktopIcon.getY(), f.getWidth(),
+ f.getHeight());
+ ourManager.deiconifyFrame(f);
+ }
+
+ void addIcon(final Container c,
+ final JInternalFrame.JDesktopIcon desktopIcon)
+ {
+ c.add(desktopIcon);
+ }
+
+ /**
+ * Removes the frame from its parent and adds its desktopIcon to the parent.
+ */
+ @Override
+ public void iconifyFrame(final JInternalFrame f)
+ {
+ ourManager.iconifyFrame(f);
+ }
+
+ // WindowsDesktopManager code
+ @Override
+ public void activateFrame(final JInternalFrame f)
+ {
+ try
+ {
+ if (f != null)
+ {
+ super.activateFrame(f);
+ }
+
+ // If this is the first activation, add to child list.
+ if (fChildFrames.indexOf(f) == -1)
+ {
+ fChildFrames.addElement(f);
+ }
+
+ if (fCurrentFrame != null && f != fCurrentFrame)
+ {
+ if (fCurrentFrame.isSelected())
+ {
+ fCurrentFrame.setSelected(false);
+ }
+ }
+
+ if (f != null && !f.isSelected())
+ {
+ f.setSelected(true);
+ }
+
+ fCurrentFrame = f;
+ } catch (final PropertyVetoException e)
+ {
+ }
+ }
+
+ private void switchFrame(final boolean next)
+ {
+ if (fCurrentFrame == null)
+ {
+ // initialize first frame we find
+ if (fInitialFrame != null)
+ {
+ activateFrame(fInitialFrame);
+ }
+ return;
+ }
+
+ final int count = fChildFrames.size();
+ if (count <= 1)
+ {
+ // No other child frames.
+ return;
+ }
+
+ final int currentIndex = fChildFrames.indexOf(fCurrentFrame);
+ if (currentIndex == -1)
+ {
+ // the "current frame" is no longer in the list
+ fCurrentFrame = null;
+ return;
+ }
+
+ int nextIndex;
+ if (next)
+ {
+ nextIndex = currentIndex + 1;
+ if (nextIndex == count)
+ {
+ nextIndex = 0;
+ }
+ }
+ else
+ {
+ nextIndex = currentIndex - 1;
+ if (nextIndex == -1)
+ {
+ nextIndex = count - 1;
+ }
+ }
+ final JInternalFrame f = fChildFrames.elementAt(nextIndex);
+ activateFrame(f);
+ fCurrentFrame = f;
+ }
+
+ /**
+ * Activate the next child JInternalFrame, as determined by the frames'
+ * Z-order. If there is only one child frame, it remains activated. If there
+ * are no child frames, nothing happens.
+ */
+ public void activateNextFrame()
+ {
+ switchFrame(true);
+ }
+
+ /**
+ * same as above but will activate a frame if none have been selected
+ */
+ public void activateNextFrame(final JInternalFrame f)
+ {
+ fInitialFrame = f;
+ switchFrame(true);
+ }
+
+ /**
+ * Activate the previous child JInternalFrame, as determined by the frames'
+ * Z-order. If there is only one child frame, it remains activated. If there
+ * are no child frames, nothing happens.
+ */
+ public void activatePreviousFrame()
+ {
+ switchFrame(false);
+ }
+ }
}
/**
+ * Answers true if range's start-end positions include those of queryRange,
+ * where either range might be in reverse direction, else false
+ *
+ * @param range
+ * a start-end range
+ * @param queryRange
+ * a candidate subrange of range (start2-end2)
+ * @return
+ */
+ public static boolean rangeContains(int[] range, int[] queryRange)
+ {
+ if (range == null || queryRange == null || range.length != 2
+ || queryRange.length != 2)
+ {
+ /*
+ * invalid arguments
+ */
+ return false;
+ }
+
+ int min = Math.min(range[0], range[1]);
+ int max = Math.max(range[0], range[1]);
+
+ return (min <= queryRange[0] && max >= queryRange[0]
+ && min <= queryRange[1] && max >= queryRange[1]);
+ }
++
++ /**
+ * Removes the specified number of positions from the given ranges. Provided
+ * to allow a stop codon to be stripped from a CDS sequence so that it matches
+ * the peptide translation length.
+ *
+ * @param positions
+ * @param ranges
+ * a list of (single) [start, end] ranges
+ * @return
+ */
+ public static void removeEndPositions(int positions,
+ List<int[]> ranges)
+ {
+ int toRemove = positions;
+ Iterator<int[]> it = new ReverseListIterator<>(ranges);
+ while (toRemove > 0)
+ {
+ int[] endRange = it.next();
+ if (endRange.length != 2)
+ {
+ /*
+ * not coded for [start1, end1, start2, end2, ...]
+ */
+ System.err
+ .println("MappingUtils.removeEndPositions doesn't handle multiple ranges");
+ return;
+ }
+
+ int length = endRange[1] - endRange[0] + 1;
+ if (length <= 0)
+ {
+ /*
+ * not coded for a reverse strand range (end < start)
+ */
+ System.err
+ .println("MappingUtils.removeEndPositions doesn't handle reverse strand");
+ return;
+ }
+ if (length > toRemove)
+ {
+ endRange[1] -= toRemove;
+ toRemove = 0;
+ }
+ else
+ {
+ toRemove -= length;
+ it.remove();
+ }
+ }
+ }
}
public class AlignmentUtilsTests
{
++ private static Sequence ts = new Sequence("short",
++ "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklm");
@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
- private static Sequence ts = new Sequence("short",
- "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklm");
-
- public static Sequence ts = new Sequence("short",
- "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklm");
-
@Test(groups = { "Functional" })
public void testExpandContext()
{
assertEquals(s_as3, uas3.getSequenceAsString());
}
+ @Test(groups = { "Functional" })
+ public void testTransferGeneLoci()
+ {
+ SequenceI from = new Sequence("transcript",
+ "aaacccgggTTTAAACCCGGGtttaaacccgggttt");
+ SequenceI to = new Sequence("CDS", "TTTAAACCCGGG");
+ MapList map = new MapList(new int[] { 1, 12 }, new int[] { 10, 21 }, 1,
+ 1);
+
+ /*
+ * first with nothing to transfer
+ */
+ AlignmentUtils.transferGeneLoci(from, map, to);
+ assertNull(to.getGeneLoci());
+
+ /*
+ * next with gene loci set on 'from' sequence
+ */
+ int[] exons = new int[] { 100, 105, 155, 164, 210, 229 };
+ MapList geneMap = new MapList(new int[] { 1, 36 }, exons, 1, 1);
+ from.setGeneLoci("human", "GRCh38", "7", geneMap);
+ AlignmentUtils.transferGeneLoci(from, map, to);
+
+ GeneLociI toLoci = to.getGeneLoci();
+ assertNotNull(toLoci);
+ // DBRefEntry constructor upper-cases 'source'
+ assertEquals("HUMAN", toLoci.getSpeciesId());
+ assertEquals("GRCh38", toLoci.getAssemblyId());
+ assertEquals("7", toLoci.getChromosomeId());
+
+ /*
+ * transcript 'exons' are 1-6, 7-16, 17-36
+ * CDS 1:12 is transcript 10-21
+ * transcript 'CDS' is 10-16, 17-21
+ * which is 'gene' 158-164, 210-214
+ */
+ MapList toMap = toLoci.getMap();
+ assertEquals(1, toMap.getFromRanges().size());
+ assertEquals(2, toMap.getFromRanges().get(0).length);
+ assertEquals(1, toMap.getFromRanges().get(0)[0]);
+ assertEquals(12, toMap.getFromRanges().get(0)[1]);
+ assertEquals(1, toMap.getToRanges().size());
+ assertEquals(4, toMap.getToRanges().get(0).length);
+ assertEquals(158, toMap.getToRanges().get(0)[0]);
+ assertEquals(164, toMap.getToRanges().get(0)[1]);
+ assertEquals(210, toMap.getToRanges().get(0)[2]);
+ assertEquals(214, toMap.getToRanges().get(0)[3]);
+ // or summarised as (but toString might change in future):
+ assertEquals("[ [1, 12] ] 1:1 to [ [158, 164, 210, 214] ]",
+ toMap.toString());
+
+ /*
+ * an existing value is not overridden
+ */
+ geneMap = new MapList(new int[] { 1, 36 }, new int[] { 36, 1 }, 1, 1);
+ from.setGeneLoci("inhuman", "GRCh37", "6", geneMap);
+ AlignmentUtils.transferGeneLoci(from, map, to);
+ assertEquals("GRCh38", toLoci.getAssemblyId());
+ assertEquals("7", toLoci.getChromosomeId());
+ toMap = toLoci.getMap();
+ assertEquals("[ [1, 12] ] 1:1 to [ [158, 164, 210, 214] ]",
+ toMap.toString());
+ }
++
+ /**
+ * Tests for the method that maps nucleotide to protein based on CDS features
+ */
+ @Test(groups = "Functional")
+ public void testMapCdsToProtein()
+ {
+ SequenceI peptide = new Sequence("pep", "KLQ");
+
+ /*
+ * Case 1: CDS 3 times length of peptide
+ * NB method only checks lengths match, not translation
+ */
+ SequenceI dna = new Sequence("dna", "AACGacgtCTCCT");
+ dna.createDatasetSequence();
+ dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
+ dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 13, null));
+ MapList ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
+ assertEquals(3, ml.getFromRatio());
+ assertEquals(1, ml.getToRatio());
+ assertEquals("[[1, 3]]",
+ Arrays.deepToString(ml.getToRanges().toArray()));
+ assertEquals("[[1, 4], [9, 13]]",
+ Arrays.deepToString(ml.getFromRanges().toArray()));
+
+ /*
+ * Case 2: CDS 3 times length of peptide + stop codon
+ * (note code does not currently check trailing codon is a stop codon)
+ */
+ dna = new Sequence("dna", "AACGacgtCTCCTTGA");
+ dna.createDatasetSequence();
+ dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
+ dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 16, null));
+ ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
+ assertEquals(3, ml.getFromRatio());
+ assertEquals(1, ml.getToRatio());
+ assertEquals("[[1, 3]]",
+ Arrays.deepToString(ml.getToRanges().toArray()));
+ assertEquals("[[1, 4], [9, 13]]",
+ Arrays.deepToString(ml.getFromRanges().toArray()));
+
+ /*
+ * Case 3: CDS not 3 times length of peptide - no mapping is made
+ */
+ dna = new Sequence("dna", "AACGacgtCTCCTTG");
+ dna.createDatasetSequence();
+ dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
+ dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 15, null));
+ ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
+ assertNull(ml);
+
+ /*
+ * Case 4: incomplete start codon corresponding to X in peptide
+ */
+ dna = new Sequence("dna", "ACGacgtCTCCTTGG");
+ dna.createDatasetSequence();
+ SequenceFeature sf = new SequenceFeature("CDS", "", 1, 3, null);
+ sf.setPhase("2"); // skip 2 positions (AC) to start of next codon (GCT)
+ dna.addSequenceFeature(sf);
+ dna.addSequenceFeature(new SequenceFeature("CDS", "", 8, 15, null));
+ peptide = new Sequence("pep", "XLQ");
+ ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
+ assertEquals("[[2, 3]]",
+ Arrays.deepToString(ml.getToRanges().toArray()));
+ assertEquals("[[3, 3], [8, 12]]",
+ Arrays.deepToString(ml.getFromRanges().toArray()));
+ }
-
}
assertEquals("[12, 11, 8, 4]", Arrays.toString(ranges));
}
+ @Test(groups = { "Functional" })
+ public void testRangeContains()
+ {
+ /*
+ * both forward ranges
+ */
+ assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+ 1, 10 }));
+ assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+ 2, 10 }));
+ assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+ 1, 9 }));
+ assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+ 4, 5 }));
+ assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+ 0, 9 }));
+ assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+ -10, -9 }));
+ assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+ 1, 11 }));
+ assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+ 11, 12 }));
+
+ /*
+ * forward range, reverse query
+ */
+ assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+ 10, 1 }));
+ assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+ 9, 1 }));
+ assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+ 10, 2 }));
+ assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+ 5, 5 }));
+ assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+ 11, 1 }));
+ assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+ 10, 0 }));
+
+ /*
+ * reverse range, forward query
+ */
+ assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+ 1, 10 }));
+ assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+ 1, 9 }));
+ assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+ 2, 10 }));
+ assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+ 6, 6 }));
+ assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+ 6, 11 }));
+ assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+ 11, 20 }));
+ assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+ -3, -2 }));
+
+ /*
+ * both reverse
+ */
+ assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+ 10, 1 }));
+ assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+ 9, 1 }));
+ assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+ 10, 2 }));
+ assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+ 3, 3 }));
+ assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+ 11, 1 }));
+ assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+ 10, 0 }));
+ assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+ 12, 11 }));
+ assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+ -5, -8 }));
+
+ /*
+ * bad arguments
+ */
+ assertFalse(MappingUtils.rangeContains(new int[] { 1, 10, 12 },
+ new int[] {
+ 1, 10 }));
+ assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 },
+ new int[] { 1 }));
+ assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, null));
+ assertFalse(MappingUtils.rangeContains(null, new int[] { 1, 10 }));
+ }
+
+ @Test(groups = "Functional")
+ public void testRemoveEndPositions()
+ {
+ List<int[]> ranges = new ArrayList<>();
+
+ /*
+ * case 1: truncate last range
+ */
+ ranges.add(new int[] { 1, 10 });
+ ranges.add(new int[] { 20, 30 });
+ MappingUtils.removeEndPositions(5, ranges);
+ assertEquals(2, ranges.size());
+ assertEquals(25, ranges.get(1)[1]);
+
+ /*
+ * case 2: remove last range
+ */
+ ranges.clear();
+ ranges.add(new int[] { 1, 10 });
+ ranges.add(new int[] { 20, 22 });
+ MappingUtils.removeEndPositions(3, ranges);
+ assertEquals(1, ranges.size());
+ assertEquals(10, ranges.get(0)[1]);
+
+ /*
+ * case 3: truncate penultimate range
+ */
+ ranges.clear();
+ ranges.add(new int[] { 1, 10 });
+ ranges.add(new int[] { 20, 21 });
+ MappingUtils.removeEndPositions(3, ranges);
+ assertEquals(1, ranges.size());
+ assertEquals(9, ranges.get(0)[1]);
+
+ /*
+ * case 4: remove last two ranges
+ */
+ ranges.clear();
+ ranges.add(new int[] { 1, 10 });
+ ranges.add(new int[] { 20, 20 });
+ ranges.add(new int[] { 30, 30 });
+ MappingUtils.removeEndPositions(3, ranges);
+ assertEquals(1, ranges.size());
+ assertEquals(9, ranges.get(0)[1]);
+ }
}
git://source.jalview.org / jalview.git / commitdiff