* mapped), we can make the scroll-to location a sequence above the one
* actually mapped.
*/
- SequenceI mappedTo = sr.getResultSequence(0);
+ SequenceI mappedTo = sr.getResults().get(0).getSequence();
List<SequenceI> seqs = av.getAlignment().getSequences();
/*
*/
package jalview.appletgui;
+import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
SequenceFeature[] features = new SequenceFeature[searchResults
.getSize()];
- for (int i = 0; i < searchResults.getSize(); i++)
+ int i = 0;
+ for (SearchResultMatchI match : searchResults.getResults())
{
- seqs[i] = searchResults.getResultSequence(i);
+ seqs[i] = match.getSequence().getDatasetSequence();
features[i] = new SequenceFeature(textfield.getText().trim(),
- "Search Results", null, searchResults.getResultStart(i),
- searchResults.getResultEnd(i), "Search Results");
+ "Search Results", null, match.getStart(), match.getEnd(),
+ "Search Results");
+ i++;
}
if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
package jalview.datamodel;
+/**
+ * An interface that describes one matched region of an alignment, as one
+ * contiguous portion of a single dataset sequence
+ */
public interface SearchResultMatchI
{
+ /**
+ * Returns the matched sequence
+ *
+ * @return
+ */
+ SequenceI getSequence();
- public abstract SequenceI getSequence();
-
- public abstract int getStart();
-
- public abstract int getEnd();
+ /**
+ * Returns the start position of the match in the sequence (base 1)
+ *
+ * @return
+ */
+ int getStart();
/**
- * Returns the string of characters in the matched region.
+ * Returns the end position of the match in the sequence (base 1)
+ *
+ * @return
*/
- public abstract String getCharacters();
+ int getEnd();
}
\ No newline at end of file
package jalview.datamodel;
import java.util.ArrayList;
-import java.util.Arrays;
import java.util.BitSet;
import java.util.List;
}
/**
- * Returns the string of characters in the matched region, prefixed by the
- * start position, e.g. "12CGT" or "208K"
+ * Returns a representation as "seqid/start-end"
*/
@Override
public String toString()
{
- final int from = Math.max(start - 1, 0);
- String startPosition = String.valueOf(from);
- return startPosition + getCharacters();
- }
-
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultMatchI#getCharacters()
- */
- @Override
- public String getCharacters()
- {
- char[] chars = sequence.getSequence();
- // convert start/end to base 0 (with bounds check)
- final int from = Math.max(start - 1, 0);
- final int to = Math.min(end, chars.length + 1);
- return String.valueOf(Arrays.copyOfRange(chars, from, to));
+ StringBuilder sb = new StringBuilder();
+ if (sequence != null)
+ {
+ sb.append(sequence.getName()).append("/");
+ }
+ sb.append(start).append("-").append(end);
+ return sb.toString();
}
public void setSequence(SequenceI seq)
public boolean involvesSequence(SequenceI sequence)
{
SequenceI ds = sequence.getDatasetSequence();
- Match m;
for (SearchResultMatchI _m : matches)
{
- m = (Match) _m;
- if (m.sequence != null
- && (m.sequence == sequence || m.sequence == ds))
+ SequenceI matched = _m.getSequence();
+ if (matched != null && (matched == sequence || matched == ds))
{
return true;
}
}
/* (non-Javadoc)
- * @see jalview.datamodel.SearchResultsI#getResultSequence(int)
- */
- @Override
- public SequenceI getResultSequence(int index)
- {
- return matches.get(index).getSequence();
- }
-
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultsI#getResultStart(int)
- */
- @Override
- public int getResultStart(int i)
- {
- return matches.get(i).getStart();
- }
-
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultsI#getResultEnd(int)
- */
- @Override
- public int getResultEnd(int i)
- {
- return matches.get(i).getEnd();
- }
-
- /* (non-Javadoc)
* @see jalview.datamodel.SearchResultsI#isEmpty()
*/
@Override
}
/**
- * Return the results as a string of characters (bases) prefixed by start
- * position(s). Meant for use when the context ensures that all matches are to
- * regions of the same sequence (otherwise the result is meaningless).
+ * Return the results as a list of matches [seq1/from-to, seq2/from-to, ...]
*
* @return
*/
@Override
public String toString()
{
- StringBuilder result = new StringBuilder(256);
- for (SearchResultMatchI m : matches)
- {
- result.append(m.toString());
- }
- return result.toString();
- }
-
- /**
- * Return the results as a string of characters (bases). Meant for use when
- * the context ensures that all matches are to regions of the same sequence
- * (otherwise the result is meaningless).
- *
- * @return
- */
- public String getCharacters()
- {
- StringBuilder result = new StringBuilder(256);
- for (SearchResultMatchI m : matches)
- {
- result.append(m.getCharacters());
- }
- return result.toString();
+ return matches == null ? "" : matches.toString();
}
/**
- * Hashcode is has derived from the list of matches. This ensures that when
- * two SearchResults objects satisfy the test for equals(), then they have the
+ * Hashcode is derived from the list of matches. This ensures that when two
+ * SearchResults objects satisfy the test for equals(), then they have the
* same hashcode.
+ *
+ * @see Match#hashCode()
+ * @see java.util.AbstractList#hashCode()
*/
@Override
public int hashCode()
package jalview.datamodel;
-
import java.util.BitSet;
import java.util.List;
+/**
+ * An interface describing the result of a search or other operation which
+ * highlights matched regions of an alignment
+ */
public interface SearchResultsI
{
/**
- * This method replaces the old search results which merely held an alignment
- * index of search matches. This broke when sequences were moved around the
- * alignment
+ * Adds one region to the results
*
* @param seq
* Sequence
* int
* @param end
* int
- * @return SearchResultMatchI instance created for this instance
+ * @return
*/
- public abstract SearchResultMatchI addResult(SequenceI seq, int start,
- int end);
+ SearchResultMatchI addResult(SequenceI seq, int start, int end);
/**
- * Quickly check if the given sequence is referred to in the search results
+ * Answers true if the search results include the given sequence (or its
+ * dataset sequence), else false
*
* @param sequence
- * (specific alignment sequence or a dataset sequence)
- * @return true if the results involve sequence
+ * @return
*/
- public abstract boolean involvesSequence(SequenceI sequence);
+ boolean involvesSequence(SequenceI sequence);
/**
- * This Method returns the search matches which lie between the start and end
- * points of the sequence in question . It is optimised for returning objects
- * for drawing on SequenceCanvas
+ * Returns an array of [from, to, from, to..] matched columns (base 0) between
+ * the given start and end columns of the given sequence. Returns null if no
+ * matches overlap the specified region.
+ * <p>
+ * Implementations should provide an optimised method to return locations to
+ * highlight on a visible portion of an alignment.
*
* @param sequence
- * sequence to highlight columns according to matches
* @param start
- * - first column of visible region
+ * first column of range (base 0, inclusive)
* @param end
- * - last column of visible region
- * @return int[] ranges within start/end index on sequence
- */
- public abstract int[] getResults(SequenceI sequence, int start, int end);
-
- public abstract int getSize();
-
- public abstract SequenceI getResultSequence(int index);
-
- /**
- * Returns the start position of the i'th match in the search results.
- *
- * @param i
- * @return
+ * last column of range base 0, inclusive)
+ * @return int[]
*/
- public abstract int getResultStart(int i);
+ int[] getResults(SequenceI sequence, int start, int end);
/**
- * Returns the end position of the i'th match in the search results.
+ * Returns the number of matches found
*
- * @param i
* @return
*/
- public abstract int getResultEnd(int i);
+ int getSize();
/**
* Returns true if no search result matches are held.
*
* @return
*/
- public abstract boolean isEmpty();
+ boolean isEmpty();
/**
* Returns the list of matches.
*
* @return
*/
- public abstract List<SearchResultMatchI> getResults();
+ List<SearchResultMatchI> getResults();
/**
* Set bits in a bitfield for all columns in the given sequence collection
* bitset to set
* @return number of bits set
*/
- public abstract int markColumns(SequenceCollectionI sqcol, BitSet bs);
+ int markColumns(SequenceCollectionI sqcol, BitSet bs);
}
\ No newline at end of file
* mapped), we can make the scroll-to location a sequence above the one
* actually mapped.
*/
- SequenceI mappedTo = sr.getResultSequence(0);
+ SequenceI mappedTo = sr.getResults().get(0).getSequence();
List<SequenceI> seqs = av.getAlignment().getSequences();
/*
*/
package jalview.gui;
+import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
SequenceFeature[] features = new SequenceFeature[searchResults
.getSize()];
- for (int i = 0; i < searchResults.getSize(); i++)
+ int i = 0;
+ for (SearchResultMatchI match : searchResults.getResults())
{
- seqs[i] = searchResults.getResultSequence(i).getDatasetSequence();
+ seqs[i] = match.getSequence().getDatasetSequence();
features[i] = new SequenceFeature(textfield.getText().trim(),
- "Search Results", null, searchResults.getResultStart(i),
- searchResults.getResultEnd(i), "Search Results");
+ "Search Results", null, match.getStart(), match.getEnd(),
+ "Search Results");
+ i++;
}
if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
+import java.util.List;
+
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
// should match seq2 efH and seq3 EFH
SearchResultsI sr = f.getSearchResults();
assertEquals(sr.getSize(), 2);
- assertSame(al.getSequenceAt(1), sr.getResultSequence(0));
- assertSame(al.getSequenceAt(2), sr.getResultSequence(1));
- assertEquals(sr.getResultStart(0), 5);
- assertEquals(sr.getResultEnd(0), 7);
- assertEquals(sr.getResultStart(1), 4);
- assertEquals(sr.getResultEnd(1), 6);
+ List<SearchResultMatchI> matches = sr.getResults();
+ assertSame(al.getSequenceAt(1), matches.get(0).getSequence());
+ assertSame(al.getSequenceAt(2), matches.get(1).getSequence());
+ assertEquals(matches.get(0).getStart(), 5);
+ assertEquals(matches.get(0).getEnd(), 7);
+ assertEquals(matches.get(1).getStart(), 4);
+ assertEquals(matches.get(1).getEnd(), 6);
}
/**
// seq1 and seq4 have 9 residues; no match in other sequences
SearchResultsI sr = f.getSearchResults();
assertEquals(sr.getSize(), 2);
- assertSame(al.getSequenceAt(0), sr.getResultSequence(0));
- assertSame(al.getSequenceAt(3), sr.getResultSequence(1));
- assertEquals(sr.getResultStart(0), 9);
- assertEquals(sr.getResultEnd(0), 9);
- assertEquals(sr.getResultStart(1), 9);
- assertEquals(sr.getResultEnd(1), 9);
+ List<SearchResultMatchI> matches = sr.getResults();
+ assertSame(al.getSequenceAt(0), matches.get(0).getSequence());
+ assertSame(al.getSequenceAt(3), matches.get(1).getSequence());
+ assertEquals(matches.get(0).getStart(), 9);
+ assertEquals(matches.get(0).getEnd(), 9);
+ assertEquals(matches.get(1).getStart(), 9);
+ assertEquals(matches.get(1).getEnd(), 9);
}
/**
f.find("e"); // matches in sequence
assertTrue(f.getIdMatch().isEmpty());
assertEquals(f.getSearchResults().getSize(), 1);
- assertEquals(f.getSearchResults().getResultStart(0), 5);
- assertEquals(f.getSearchResults().getResultEnd(0), 5);
- assertSame(f.getSearchResults().getResultSequence(0),
- al.getSequenceAt(1));
+ List<SearchResultMatchI> matches = f.getSearchResults().getResults();
+ assertEquals(matches.get(0).getStart(), 5);
+ assertEquals(matches.get(0).getEnd(), 5);
+ assertSame(matches.get(0).getSequence(), al.getSequenceAt(1));
// still in the second sequence
assertEquals(f.getSeqIndex(), 1);
// next residue position to search from is 5
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
-import jalview.datamodel.SearchResults.Match;
-
import org.testng.annotations.Test;
public class MatchTest
@Test(groups = { "Functional" })
public void testToString()
{
- SequenceI seq = new Sequence("", "abcdefghijklm");
- SearchResultMatchI m = new SearchResults().new Match(seq, 3, 5);
- assertEquals("2cde", m.toString());
- }
-
- @Test(groups = { "Functional" })
- public void testGetCharacters()
- {
- SequenceI seq = new Sequence("", "abcdefghijklm");
+ SequenceI seq = new Sequence("Seq1", "abcdefghijklm");
SearchResultMatchI m = new SearchResults().new Match(seq, 3, 5);
- assertEquals("cde", m.getCharacters());
+ assertEquals("Seq1/3-5", m.toString());
}
@Test(groups = { "Functional" })
@Test(groups = { "Functional" })
public void testToString()
{
- SequenceI seq = new Sequence("", "abcdefghijklm");
+ SequenceI seq = new Sequence("Seq1", "abcdefghijklm");
SearchResultsI sr = new SearchResults();
sr.addResult(seq, 1, 1);
- assertEquals("0a", sr.toString());
+ assertEquals("[Seq1/1-1]", sr.toString());
sr.addResult(seq, 3, 5);
- assertEquals("0a2cde", sr.toString());
+ assertEquals("[Seq1/1-1, Seq1/3-5]", sr.toString());
- seq = new Sequence("", "pqrstuvwxy");
+ seq = new Sequence("Seq2", "pqrstuvwxy");
sr.addResult(seq, 6, 7);
- assertEquals("0a2cde5uv", sr.toString());
- }
-
- @Test(groups = { "Functional" })
- public void testGetCharacters()
- {
- SequenceI seq = new Sequence("", "abcdefghijklm");
- SearchResults sr = new SearchResults();
- sr.addResult(seq, 1, 1);
- assertEquals("a", sr.getCharacters());
- sr.addResult(seq, 3, 5);
- assertEquals("acde", sr.getCharacters());
-
- seq = new Sequence("", "pqrstuvwxy");
- sr.addResult(seq, 6, 7);
- assertEquals("acdeuv", sr.getCharacters());
+ assertEquals("[Seq1/1-1, Seq1/3-5, Seq2/6-7]", sr.toString());
}
@Test(groups = { "Functional" })
assertTrue(sr2.equals(sr1)); // reflexive
/*
- * only one result is not empty
+ * if only one result is not empty
*/
sr1.addResult(seq1, 1, 1);
assertTrue(sr1.equals(sr1));
git://source.jalview.org / jalview.git / commitdiff