From 2ca081eebf90c6731cd79bde140ca2fecc9c9644 Mon Sep 17 00:00:00 2001 From: kiramt Date: Wed, 29 Mar 2017 10:51:59 +0100 Subject: [PATCH] JAL-2388 New iterators and tests --- src/jalview/datamodel/AllColsIterator.java | 77 +++++++ src/jalview/datamodel/AllRowsIterator.java | 77 +++++++ src/jalview/datamodel/VisibleColsIterator.java | 131 +++++++++++ src/jalview/datamodel/VisibleRowsIterator.java | 99 +++++++++ test/jalview/datamodel/AllColsIteratorTest.java | 85 +++++++ test/jalview/datamodel/AllRowsIteratorTest.java | 113 ++++++++++ .../jalview/datamodel/VisibleColsIteratorTest.java | 198 +++++++++++++++++ .../jalview/datamodel/VisibleRowsIteratorTest.java | 233 ++++++++++++++++++++ 8 files changed, 1013 insertions(+) create mode 100644 src/jalview/datamodel/AllColsIterator.java create mode 100644 src/jalview/datamodel/AllRowsIterator.java create mode 100644 src/jalview/datamodel/VisibleColsIterator.java create mode 100644 src/jalview/datamodel/VisibleRowsIterator.java create mode 100644 test/jalview/datamodel/AllColsIteratorTest.java create mode 100644 test/jalview/datamodel/AllRowsIteratorTest.java create mode 100644 test/jalview/datamodel/VisibleColsIteratorTest.java create mode 100644 test/jalview/datamodel/VisibleRowsIteratorTest.java diff --git a/src/jalview/datamodel/AllColsIterator.java b/src/jalview/datamodel/AllColsIterator.java new file mode 100644 index 0000000..4e1ff2e --- /dev/null +++ b/src/jalview/datamodel/AllColsIterator.java @@ -0,0 +1,77 @@ +/* + * 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. + * + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.datamodel; + +import java.util.Iterator; +import java.util.NoSuchElementException; + +/** + * An iterator which iterates over all columns or rows in an alignment, whether + * hidden or visible. + * + * @author kmourao + * + */ +public class AllColsIterator implements Iterator +{ + private int last; + + private int next; + + private int current; + + ColumnSelection hidden; + + public AllColsIterator(int firstcol, int lastcol, + ColumnSelection hiddenCols) + { + last = lastcol; + next = firstcol; + current = firstcol; + hidden = hiddenCols; + } + + @Override + public boolean hasNext() + { + return current + 1 <= last; + } + + @Override + public Integer next() + { + if (current + 1 > last) + { + throw new NoSuchElementException(); + } + current = next; + next++; + + return current; + } + + @Override + public void remove() + { + throw new UnsupportedOperationException(); + } +} + diff --git a/src/jalview/datamodel/AllRowsIterator.java b/src/jalview/datamodel/AllRowsIterator.java new file mode 100644 index 0000000..aefed60 --- /dev/null +++ b/src/jalview/datamodel/AllRowsIterator.java @@ -0,0 +1,77 @@ +/* + * 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. + * + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.datamodel; + +import java.util.Iterator; +import java.util.NoSuchElementException; + +/** + * An iterator which iterates over all columns or rows in an alignment, whether + * hidden or visible. + * + * @author kmourao + * + */ +public class AllRowsIterator implements Iterator +{ + private int last; + + private int next; + + private int current; + + private AlignmentI al; + + public AllRowsIterator(int firstrow, int lastrow, AlignmentI alignment) + { + last = lastrow; + current = firstrow; + next = firstrow; + al = alignment; + } + + @Override + public boolean hasNext() + { + return current + 1 <= last; + } + + @Override + public Integer next() + { + if (current + 1 > last) + { + throw new NoSuchElementException(); + } + current = next; + next++; + + return current; + } + + @Override + public void remove() + { + throw new UnsupportedOperationException(); + } +} + + diff --git a/src/jalview/datamodel/VisibleColsIterator.java b/src/jalview/datamodel/VisibleColsIterator.java new file mode 100644 index 0000000..2a69a82 --- /dev/null +++ b/src/jalview/datamodel/VisibleColsIterator.java @@ -0,0 +1,131 @@ +/* + * 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. + * + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.datamodel; + +import java.util.Iterator; +import java.util.List; +import java.util.NoSuchElementException; + +/** + * An iterator which iterates over all visible columns in an alignment + * + * @author kmourao + * + */ +public class VisibleColsIterator implements Iterator +{ + private int last; + + private int current; + + private int next; + + private List hidden; + + private int lasthiddenregion; + + public VisibleColsIterator(int firstcol, int lastcol, + ColumnSelection hiddenCols) + { + last = lastcol; + current = firstcol; + next = firstcol; + hidden = hiddenCols.getHiddenColumns(); + lasthiddenregion = -1; + + if (hidden != null) + { + int i = 0; + for (i = 0; i < hidden.size(); ++i) + { + if (current >= hidden.get(i)[0] && current <= hidden.get(i)[1]) + { + // current is hidden, move to right + current = hidden.get(i)[1] + 1; + next = current; + } + if (current < hidden.get(i)[0]) + { + break; + } + } + lasthiddenregion = i - 1; + + for (i = hidden.size() - 1; i >= 0; --i) + { + if (last >= hidden.get(i)[0] && last <= hidden.get(i)[1]) + { + // last is hidden, move to left + last = hidden.get(i)[0] - 1; + } + if (last > hidden.get(i)[1]) + { + break; + } + } + } + } + + @Override + public boolean hasNext() + { + return next <= last; + } + + @Override + public Integer next() + { + if (next > last) + { + throw new NoSuchElementException(); + } + current = next; + if ((hidden != null) && (lasthiddenregion + 1 < hidden.size())) + { + // still some more hidden regions + if (next + 1 < hidden.get(lasthiddenregion + 1)[0]) + { + // next+1 is still before the next hidden region + next++; + } + else if ((next + 1 >= hidden.get(lasthiddenregion + 1)[0]) + && (next + 1 <= hidden.get(lasthiddenregion + 1)[1])) + { + // next + 1 is in the next hidden region + next = hidden.get(lasthiddenregion + 1)[1] + 1; + lasthiddenregion++; + } + } + else + { + // finished with hidden regions, just increment normally + next++; + } + return current; + } + + @Override + public void remove() + { + throw new UnsupportedOperationException(); + } +} + diff --git a/src/jalview/datamodel/VisibleRowsIterator.java b/src/jalview/datamodel/VisibleRowsIterator.java new file mode 100644 index 0000000..0259fd3 --- /dev/null +++ b/src/jalview/datamodel/VisibleRowsIterator.java @@ -0,0 +1,99 @@ +/* + * 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. + * + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.datamodel; + +import java.util.Iterator; +import java.util.NoSuchElementException; + +/** + * An iterator which iterates over all visible rows in an alignment + * + * @author kmourao + * + */ +public class VisibleRowsIterator implements Iterator +{ + private int last; + + private int current; + + private int next; + + private HiddenSequences hidden; + + private AlignmentI al; + + /** + * Create an iterator for all visible rows in the alignment + * + * @param firstrow + * absolute row index to start from + * @param lastrow + * absolute row index to end at + * @param alignment + * alignment to work with + */ + public VisibleRowsIterator(int firstrow, int lastrow, AlignmentI alignment) + { + al = alignment; + current = firstrow; + last = lastrow; + hidden = al.getHiddenSequences(); + while (hidden.isHidden(last) && last > current) + { + last--; + } + current = firstrow; + while (hidden.isHidden(current) && current < last) + { + current++; + } + next = current; + } + + @Override + public boolean hasNext() + { + return next <= last; + } + + @Override + public Integer next() + { + if (next > last) + { + throw new NoSuchElementException(); + } + current = next; + do + { + next++; + } while (hidden.isHidden(next) && next <= last); + return current; + } + + @Override + public void remove() + { + throw new UnsupportedOperationException(); + } +} + diff --git a/test/jalview/datamodel/AllColsIteratorTest.java b/test/jalview/datamodel/AllColsIteratorTest.java new file mode 100644 index 0000000..ee82340 --- /dev/null +++ b/test/jalview/datamodel/AllColsIteratorTest.java @@ -0,0 +1,85 @@ +/* + * 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. + * + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.datamodel; + +import static org.testng.Assert.assertTrue; + +import java.util.NoSuchElementException; + +import org.testng.annotations.BeforeClass; +import org.testng.annotations.Test; + +public class AllColsIteratorTest +{ + ColumnSelection hiddenCols; + + @BeforeClass + public void setup() + { + hiddenCols = new ColumnSelection(); + hiddenCols.hideColumns(2,4); + } + + + /* + * Test iterator iterates through collection correctly + */ + @Test(groups = { "Functional" }) + public void testHasNextAndNext() + { + AllColsIterator it = new AllColsIterator(0, 3, hiddenCols); + int count = 0; + while (it.hasNext()) + { + it.next(); + count++; + } + assertTrue(count == 4, "hasNext() is false after 4 iterations"); + } + + /* + * Test iterator throws NoSuchElementException at end of iteration + */ + @Test( + groups = { "Functional" }, + expectedExceptions = { NoSuchElementException.class }) + public void testLastNext() throws NoSuchElementException + { + AllColsIterator it = new AllColsIterator(0, 3, hiddenCols); + while (it.hasNext()) + { + it.next(); + } + it.next(); + } + + /* + * Test iterator throws UnsupportedOperationException on call to remove + */ + @Test( + groups = { "Functional" }, + expectedExceptions = { UnsupportedOperationException.class }) + public void testRemove() throws UnsupportedOperationException + { + AllColsIterator it = new AllColsIterator(0, 3, hiddenCols); + it.remove(); + } +} diff --git a/test/jalview/datamodel/AllRowsIteratorTest.java b/test/jalview/datamodel/AllRowsIteratorTest.java new file mode 100644 index 0000000..fd1d29d --- /dev/null +++ b/test/jalview/datamodel/AllRowsIteratorTest.java @@ -0,0 +1,113 @@ +/* + * 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. + * + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.datamodel; + +import static org.testng.Assert.assertTrue; + +import jalview.analysis.AlignmentGenerator; + +import java.util.Hashtable; +import java.util.NoSuchElementException; + +import org.testng.annotations.BeforeClass; +import org.testng.annotations.Test; + +public class AllRowsIteratorTest +{ + AlignmentI al; + + Hashtable hiddenRepSequences = new Hashtable(); + + @BeforeClass + public void setup() + { + // create random alignment + AlignmentGenerator gen = new AlignmentGenerator(false); + al = gen.generate(20, 15, 123, 5, 5); + if (!hiddenRepSequences.isEmpty()) + { + al.getHiddenSequences().showAll(hiddenRepSequences); + } + hideSequences(2, 4); + } + + /* + * Test iterator iterates through collection correctly + */ + @Test(groups = { "Functional" }) + public void testHasNextAndNext() + { + AllRowsIterator it = new AllRowsIterator(0, 3, al); + int count = 0; + while (it.hasNext()) + { + it.next(); + count++; + } + assertTrue(count == 4, "hasNext() is false after 4 iterations"); + } + + /* + * Test iterator throws NoSuchElementException at end of iteration + */ + @Test( + groups = { "Functional" }, + expectedExceptions = { NoSuchElementException.class }) + public void testLastNext() throws NoSuchElementException + { + AllRowsIterator it = new AllRowsIterator(0, 3, al); + while (it.hasNext()) + { + it.next(); + } + it.next(); + } + + /* + * Test iterator throws UnsupportedOperationException on call to remove + */ + @Test( + groups = { "Functional" }, + expectedExceptions = { UnsupportedOperationException.class }) + public void testRemove() throws UnsupportedOperationException + { + AllRowsIterator it = new AllRowsIterator(0, 3, al); + it.remove(); + } + + + /* + * Hide sequences between start and end + */ + private void hideSequences(int start, int end) + { + SequenceI[] allseqs = al.getSequencesArray(); + SequenceGroup theseSeqs = new SequenceGroup(); + + for (int i = start; i <= end; i++) + { + theseSeqs.addSequence(allseqs[i], false); + al.getHiddenSequences().hideSequence(allseqs[i]); + } + + hiddenRepSequences.put(allseqs[start], theseSeqs); + } +} diff --git a/test/jalview/datamodel/VisibleColsIteratorTest.java b/test/jalview/datamodel/VisibleColsIteratorTest.java new file mode 100644 index 0000000..c07b3c9 --- /dev/null +++ b/test/jalview/datamodel/VisibleColsIteratorTest.java @@ -0,0 +1,198 @@ +/* + * 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. + * + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.datamodel; + +import static org.testng.Assert.assertTrue; + +import java.util.NoSuchElementException; + +import org.testng.annotations.BeforeClass; +import org.testng.annotations.Test; + +public class VisibleColsIteratorTest +{ + ColumnSelection hiddenCols; + + ColumnSelection hiddenColsAtStart; + + @BeforeClass + public void setup() + { + hiddenCols = new ColumnSelection(); + hiddenCols.hideColumns(2, 4); + + hiddenColsAtStart = new ColumnSelection(); + hiddenColsAtStart.hideColumns(0, 2); + } + + /* + * Test iterator iterates correctly through the columns + * when alignment has hidden cols + */ + @Test(groups = { "Functional" }) + public void testHasNextAndNextWithHidden() + { + VisibleColsIterator it = new VisibleColsIterator(0, 6, hiddenCols); + int count = 0; + while (it.hasNext()) + { + it.next(); + count++; + } + assertTrue(count == 4, "hasNext() is false after 4 iterations"); + } + + /* + * Test iterator iterates correctly through the columns + * when alignment has no hidden cols + */ + @Test(groups = { "Functional" }) + public void testHasNextAndNextNoHidden() + { + VisibleColsIterator it2 = new VisibleColsIterator(0, 3, + new ColumnSelection()); + int count = 0; + while (it2.hasNext()) + { + it2.next(); + count++; + } + assertTrue(count == 4, "hasNext() is false after 4 iterations"); + } + + /* + * Test iterator iterates correctly through the columns + * when alignment has hidden cols at start + */ + @Test(groups = { "Functional" }) + public void testHasNextAndNextStartHidden() + { + VisibleColsIterator it3 = new VisibleColsIterator(0, 6, + hiddenColsAtStart); + int count = 0; + while (it3.hasNext()) + { + it3.next(); + count++; + } + assertTrue(count == 4, "hasNext() is false after 4 iterations"); + } + + /* + * Test iterator iterates correctly through the columns + * when alignment has hidden cols at end + */ + @Test(groups = { "Functional" }) + public void testHasNextAndNextEndHidden() + { + VisibleColsIterator it4 = new VisibleColsIterator(0, 4, hiddenCols); + int count = 0; + while (it4.hasNext()) + { + it4.next(); + count++; + } + assertTrue(count == 2, "hasNext() is false after 2 iterations"); + + } + + /* + * Test iterator always throws NoSuchElementException at end of iteration + * when alignment has hidden cols + */ + @Test( + groups = { "Functional" }, + expectedExceptions = { NoSuchElementException.class }) + public void testLastNextWithHidden() throws NoSuchElementException + { + VisibleColsIterator it = new VisibleColsIterator(0, 3, hiddenCols); + while (it.hasNext()) + { + it.next(); + } + it.next(); + } + + /* + * Test iterator always throws NoSuchElementException at end of iteration + * when alignment has no hidden cols + */ + @Test( + groups = { "Functional" }, + expectedExceptions = { NoSuchElementException.class }) + public void testLastNextNoHidden() throws NoSuchElementException + { + VisibleColsIterator it2 = new VisibleColsIterator(0, 3, + new ColumnSelection()); + while (it2.hasNext()) + { + it2.next(); + } + it2.next(); + } + + /* + * Test iterator always throws NoSuchElementException at end of iteration + * when alignment has hidden cols at start + */ + @Test( + groups = { "Functional" }, + expectedExceptions = { NoSuchElementException.class }) + public void testLastNextStartHidden() throws NoSuchElementException + { + VisibleColsIterator it3 = new VisibleColsIterator(0, 6, + hiddenColsAtStart); + while (it3.hasNext()) + { + it3.next(); + } + it3.next(); + } + + /* + * Test iterator always throws NoSuchElementException at end of iteration + * when alignment has hidden cols at end + */ + @Test( + groups = { "Functional" }, + expectedExceptions = { NoSuchElementException.class }) + public void testLastNextEndHidden() throws NoSuchElementException + { + VisibleColsIterator it4 = new VisibleColsIterator(0, 4, hiddenCols); + while (it4.hasNext()) + { + it4.next(); + } + it4.next(); + } + + /* + * Test calls to remove throw UnsupportedOperationException + */ + @Test( + groups = { "Functional" }, + expectedExceptions = { UnsupportedOperationException.class }) + public void testRemove() throws UnsupportedOperationException + { + VisibleColsIterator it = new VisibleColsIterator(0, 3, hiddenCols); + it.remove(); + } +} diff --git a/test/jalview/datamodel/VisibleRowsIteratorTest.java b/test/jalview/datamodel/VisibleRowsIteratorTest.java new file mode 100644 index 0000000..da93dab --- /dev/null +++ b/test/jalview/datamodel/VisibleRowsIteratorTest.java @@ -0,0 +1,233 @@ +/* + * 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. + * + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.datamodel; + +import static org.testng.Assert.assertTrue; + +import jalview.analysis.AlignmentGenerator; + +import java.util.Hashtable; +import java.util.NoSuchElementException; + +import org.testng.annotations.BeforeClass; +import org.testng.annotations.Test; + +public class VisibleRowsIteratorTest +{ + AlignmentI al; + + AlignmentI al2; + + AlignmentI al3; + + Hashtable hiddenRepSequences = new Hashtable(); + + Hashtable hiddenRepSequences2 = new Hashtable(); + + @BeforeClass + public void setup() + { + // create random alignment + AlignmentGenerator gen = new AlignmentGenerator(false); + al = gen.generate(20, 15, 123, 5, 5); + if (!hiddenRepSequences.isEmpty()) + { + al.getHiddenSequences().showAll(hiddenRepSequences); + } + hideSequences(al, hiddenRepSequences, 2, 4); + + al2 = gen.generate(20, 15, 123, 5, 5); + if (!hiddenRepSequences2.isEmpty()) + { + al2.getHiddenSequences().showAll(hiddenRepSequences2); + } + hideSequences(al2, hiddenRepSequences2, 0, 2); + + al3 = gen.generate(20, 15, 123, 5, 5); + } + + /* + * Test iterator iterates correctly through the rows + * when alignment has hidden rows + */ + @Test(groups = { "Functional" }) + public void testHasNextAndNextWithHidden() + { + VisibleRowsIterator it = new VisibleRowsIterator(0, 6, al); + int count = 0; + while (it.hasNext()) + { + it.next(); + count++; + } + assertTrue(count == 4, "hasNext() is false after 4 iterations"); + } + + /* + * Test iterator iterates correctly through the rows + * when alignment has no hidden rows + */ + @Test(groups = { "Functional" }) + public void testHasNextAndNextNoHidden() + { + VisibleRowsIterator it = new VisibleRowsIterator(0, 3, al3); + int count = 0; + while (it.hasNext()) + { + it.next(); + count++; + } + assertTrue(count == 4, "hasNext() is false after 4 iterations"); + } + + /* + * Test iterator iterates correctly through the rows + * when alignment has hidden rows at start + */ + @Test(groups = { "Functional" }) + public void testHasNextAndNextStartHidden() + { + VisibleRowsIterator it = new VisibleRowsIterator(0, 6, al2); + int count = 0; + while (it.hasNext()) + { + it.next(); + count++; + } + assertTrue(count == 4, "hasNext() is false after 4 iterations"); + } + + /* + * Test iterator iterates correctly through the rows + * when alignment has hidden rows at end + */ + @Test(groups = { "Functional" }) + public void testHasNextAndNextEndHidden() + { + VisibleRowsIterator it = new VisibleRowsIterator(0, 4, al); + int count = 0; + while (it.hasNext()) + { + it.next(); + count++; + } + assertTrue(count == 2, "hasNext() is false after 2 iterations"); + } + + /* + * Test iterator always throws NoSuchElementException at end of iteration + * when alignment has hidden rows + */ + @Test( + groups = { "Functional" }, + expectedExceptions = { NoSuchElementException.class }) + public void testLastNextWithHidden() throws NoSuchElementException + { + VisibleRowsIterator it = new VisibleRowsIterator(0, 3, al); + while (it.hasNext()) + { + it.next(); + } + it.next(); + } + + /* + * Test iterator always throws NoSuchElementException at end of iteration + * when alignment has no hidden rows + */ + @Test( + groups = { "Functional" }, + expectedExceptions = { NoSuchElementException.class }) + public void testLastNextNoHidden() throws NoSuchElementException + { + VisibleRowsIterator it = new VisibleRowsIterator(0, 3, al3); + while (it.hasNext()) + { + it.next(); + } + it.next(); + } + + /* + * Test iterator always throws NoSuchElementException at end of iteration + * when alignment has hidden rows at start + */ + @Test( + groups = { "Functional" }, + expectedExceptions = { NoSuchElementException.class }) + public void testLastNextStartHidden() throws NoSuchElementException + { + VisibleRowsIterator it = new VisibleRowsIterator(0, 3, al2); + while (it.hasNext()) + { + it.next(); + } + it.next(); + } + + /* + * Test iterator always throws NoSuchElementException at end of iteration + * when alignment has hidden rows at end + */ + @Test( + groups = { "Functional" }, + expectedExceptions = { NoSuchElementException.class }) + public void testLastNextEndHidden() throws NoSuchElementException + { + VisibleRowsIterator it = new VisibleRowsIterator(0, 4, al); + while (it.hasNext()) + { + it.next(); + } + it.next(); + } + + /* + * Test calls to remove throw UnsupportedOperationException + */ + @Test( + groups = { "Functional" }, + expectedExceptions = { UnsupportedOperationException.class }) + public void testRemove() throws UnsupportedOperationException + { + VisibleRowsIterator it = new VisibleRowsIterator(0, 3, al); + it.remove(); + } + + /* + * Hide sequences between start and end + */ + private void hideSequences(AlignmentI alignment, + Hashtable hiddenRepSequences, + int start, int end) + { + SequenceI[] allseqs = alignment.getSequencesArray(); + SequenceGroup theseSeqs = new SequenceGroup(); + + for (int i = start; i <= end; i++) + { + theseSeqs.addSequence(allseqs[i], false); + alignment.getHiddenSequences().hideSequence(allseqs[i]); + } + + hiddenRepSequences.put(allseqs[start], theseSeqs); + } +} -- 1.7.10.2