package jalview.datamodel;
import jalview.schemes.ResidueProperties;
+import jalview.util.Comparison;
import java.util.ArrayList;
import java.util.HashMap;
// contains the HMM node for each alignment column, alignment columns start at
// index 0;
- Map<Integer, Integer> nodeLookup = new HashMap<>();
+ Map<Integer, HMMNode> nodeLookup = new HashMap<>();
// contains the symbol index for each symbol
Map<Character, Integer> symbolIndexLookup = new HashMap<>();
final static String NO = "no";
// keys for file properties hashmap
- private final String NAME = "NAME";
+ private static final String NAME = "NAME";
- private final String ACCESSION_NUMBER = "ACC";
+ private static final String ACCESSION_NUMBER = "ACC";
- private final String DESCRIPTION = "DESC";
+ private static final String DESCRIPTION = "DESC";
- private final String LENGTH = "LENG";
+ private static final String LENGTH = "LENG";
- private final String MAX_LENGTH = "MAXL";
+ private static final String MAX_LENGTH = "MAXL";
- private final String ALPHABET = "ALPH";
+ private static final String ALPHABET = "ALPH";
- private final String DATE = "DATE";
+ private static final String DATE = "DATE";
- private final String COMMAND_LOG = "COM";
+ private static final String COMMAND_LOG = "COM";
- private final String NUMBER_OF_SEQUENCES = "NSEQ";
+ private static final String NUMBER_OF_SEQUENCES = "NSEQ";
- private final String EFF_NUMBER_OF_SEQUENCES = "EFFN";
+ private static final String EFF_NUMBER_OF_SEQUENCES = "EFFN";
- private final String CHECK_SUM = "CKSUM";
+ private static final String CHECK_SUM = "CKSUM";
- private final String GATHERING_THRESHOLDS = "GA";
+ private static final String GATHERING_THRESHOLDS = "GA";
- private final String TRUSTED_CUTOFFS = "TC";
+ private static final String TRUSTED_CUTOFFS = "TC";
- private final String NOISE_CUTOFFS = "NC";
+ private static final String NOISE_CUTOFFS = "NC";
- private final String STATISTICS = "STATS";
+ private static final String STATISTICS = "STATS";
- private final String COMPO = "COMPO";
+ private static final String COMPO = "COMPO";
- private final String GATHERING_THRESHOLD = "GA";
+ private static final String GATHERING_THRESHOLD = "GA";
- private final String TRUSTED_CUTOFF = "TC";
+ private static final String TRUSTED_CUTOFF = "TC";
private final String NOISE_CUTOFF = "NC";
- private final String VITERBI = "VITERBI";
+ private static final String VITERBI = "VITERBI";
- private final String MSV = "MSV";
+ private static final String MSV = "MSV";
- private final String FORWARD = "FORWARD";
+ private static final String FORWARD = "FORWARD";
- private final String MAP = "MAP";
+ private static final String MAP = "MAP";
- private final String REFERENCE_ANNOTATION = "RF";
+ private static final String REFERENCE_ANNOTATION = "RF";
- private final String CONSENSUS_RESIDUE = "CONS";
+ private static final String CONSENSUS_RESIDUE = "CONS";
- private final String CONSENSUS_STRUCTURE = "CS";
+ private static final String CONSENSUS_STRUCTURE = "CS";
- private final String MASKED_VALUE = "MM";
+ private static final String MASKED_VALUE = "MM";
public static final int MATCHTOMATCH = 0;
* @return
*
*/
- public Map<Integer, Integer> getNodeLookup()
+ public Map<Integer, HMMNode> getNodeLookup()
{
return nodeLookup;
}
*/
public double getMatchEmissionProbability(int alignColumn, char symbol)
{
- int symbolIndex;
- int nodeIndex;
- double probability;
if (!symbolIndexLookup.containsKey(symbol))
{
return 0d;
}
- symbolIndex = symbolIndexLookup.get(symbol);
+ int symbolIndex = symbolIndexLookup.get(symbol);
+ double probability = 0d;
if (nodeLookup.containsKey(alignColumn))
{
- nodeIndex = nodeLookup.get(alignColumn);
- probability = getNode(nodeIndex).getMatchEmissions().get(symbolIndex);
- return probability;
- }
- else
- {
- return 0d;
+ HMMNode node = nodeLookup.get(alignColumn);
+ probability = node.getMatchEmissions().get(symbolIndex);
}
+ return probability;
}
/**
*/
public double getInsertEmissionProbability(int alignColumn, char symbol)
{
- int symbolIndex;
- int nodeIndex;
- double probability;
if (!symbolIndexLookup.containsKey(symbol))
{
return 0d;
}
- symbolIndex = symbolIndexLookup.get(symbol);
+ int symbolIndex = symbolIndexLookup.get(symbol);
+ double probability = 0d;
if (nodeLookup.containsKey(alignColumn))
{
- nodeIndex = nodeLookup.get(alignColumn);
- probability = getNode(nodeIndex).getInsertEmissions()
- .get(symbolIndex);
- return probability;
- }
- else
- {
- return 0d;
+ HMMNode node = nodeLookup.get(alignColumn);
+ probability = node.getInsertEmissions().get(symbolIndex);
}
-
+ return probability;
}
/**
public Double getStateTransitionProbability(int alignColumn,
int transition)
{
- int nodeIndex;
- Double probability;
+ double probability = 0d;
if (nodeLookup.containsKey(alignColumn))
{
- nodeIndex = nodeLookup.get(alignColumn);
- probability = getNode(nodeIndex).getStateTransitions()
- .get(transition);
- return probability;
+ HMMNode node = nodeLookup.get(alignColumn);
+ probability = node.getStateTransitions().get(transition);
}
- else
- {
- return 0d;
- }
-
+ return probability;
}
/**
char mostLikely = '-';
if (consensusResidueIsActive())
{
-
- Integer index = findNodeIndex(columnIndex);
- if (index == null)
- {
- return '-';
- }
- mostLikely = getNodes().get(index).getConsensusResidue();
+ HMMNode node = nodeLookup.get(columnIndex);
+ if (node == null)
+ {
+ return '-';
+ }
+ mostLikely = node.getConsensusResidue();
return mostLikely;
}
else
double highestProb = 0;
for (char character : symbols)
{
- Double prob = getMatchEmissionProbability(columnIndex, character);
+ double prob = getMatchEmissionProbability(columnIndex, character);
if (prob > highestProb)
{
highestProb = prob;
}
/**
- * Sets the alignment column of the specified node.
+ * Sets the alignment column of the specified node
*
* @param nodeIndex
*
* @param column
*
*/
- public void setAlignmentColumn(int nodeIndex, int column)
+ public void setAlignmentColumn(HMMNode node, int column)
{
- nodes.get(nodeIndex).setAlignmentColumn(column);
- nodeLookup.put(column, nodeIndex);
+ node.setAlignmentColumn(column);
+ nodeLookup.put(column, node);
+ }
+
+ public void updateMapping(char[] sequence)
+ {
+ int nodeNo = 1;
+ int column = 0;
+ synchronized (nodeLookup)
+ {
+ clearNodeLookup();
+ for (char residue : sequence)
+ {
+ if (!Comparison.isGap(residue))
+ {
+ HMMNode node = nodes.get(nodeNo);
+ if (node == null)
+ {
+ // error : too few nodes for sequence
+ break;
+ }
+ setAlignmentColumn(node, column);
+ nodeNo++;
+ }
+ column++;
+ }
+ }
}
/**
* Clears all data in the node lookup map
*/
- public void emptyNodeLookup()
+ public void clearNodeLookup()
{
- nodeLookup = new HashMap<>();
+ nodeLookup.clear();
}
-
/**
* Sets the reference annotation at a given node.
*
}
/**
- * Finds the index of the node in a hidden Markov model based on the column in
- * the alignment
+ * Answers the HMMNode mapped to the given alignment column (base 0), or null
+ * if none is mapped
*
* @param alignmentColumn
- * The index of the column in the alignment, with the indexes
- * starting from 0.
*/
-
- public Integer findNodeIndex(int alignmentColumn)
+ public HMMNode getNodeForColumn(int alignmentColumn)
{
- Integer index;
- index = nodeLookup.get(alignmentColumn);
- return index;
+ return nodeLookup.get(alignmentColumn);
}
/**
@Override
public void updateHMMMapping()
{
- int node = 1;
- int column = 0;
- hmm.emptyNodeLookup();
- for (char residue : sequence)
+ if (hmm == null)
{
- if (!Comparison.isGap(residue))
- {
- hmm.setAlignmentColumn(node, column);
- node++;
- }
- column++;
+ return;
}
+ hmm.updateMapping(sequence);
}
/**
if (this.isHMMConsensusSequence)
{
int node = 1;
- hmm.emptyNodeLookup();
+ hmm.clearNodeLookup();
for (int i = 0; i < getLength(); i++)
{
if (rf.annotations[i].displayCharacter.equals("x")
*/
public List<DBRefEntry> getPrimaryDBRefs();
+ /**
+ * Updates mapping of Hidden Markov Model nodes to aligned sequence positions
+ * (e.g. after an alignment edit). The nodes of the HMM (excluding the first
+ * node, with model average values), are associated in turn with non-gapped
+ * sequence positions.
+ */
public void updateHMMMapping();
boolean isHMMConsensusSequence();
public void run()
{
hmm = af.getSelectedHMM();
+ if (hmm == null)
+ {
+ System.err.println("Can't run hmmalign as no HMM profile selected");
+ return;
+ }
long msgId = System.currentTimeMillis();
af.setProgressBar(MessageManager.getString("status.running_hmmalign"),
AlignViewportI viewport = af.getViewport();
try
{
+ if (viewport != null)
+ {
+ alignment = viewport.getAlignment();
+ }
List<SequenceGroup> groups = new ArrayList<>();
if (params != null)
{
}
}
}
- else if (viewport != null)
- {
- alignment = viewport.getAlignment();
- }
if (alignment != null)
{
public class HMMFile extends AlignFile
implements AlignmentFileReaderI, AlignmentFileWriterI
{
- // HMM to store file data
- private HiddenMarkovModel hmm;
-
- // number of possible transitions
private static final int NUMBER_OF_TRANSITIONS = 7;
- private String NL = "\n";
+ private static final String SPACE = " ";
- //number of symbols in the alphabet used in the hidden Markov model
- int numberOfSymbols;
+ private static final String COMPO = "COMPO";
- private final String SPACE = " ";
+ private static final String EMPTY = "";
- private final String COMPO = "COMPO";
+ /*
+ * guide line added to an output HMMER file, purely for readability
+ */
+ private static final String TRANSITIONTYPELINE = " m->m m->i m->d i->m i->i d->m d->d";
- private final String EMPTY = "";
+ private static String NL = "\n";
- //This is a line that needs to be added to each HMMER� file. It is purely for readability.
- private static final String TRANSITIONTYPELINE = " m->m m->i m->d i->m i->i d->m d->d";
+ private HiddenMarkovModel hmm;
+
+ // number of symbols in the alphabet used in the hidden Markov model
+ int numberOfSymbols;
/**
* Parses immediately.
*/
void parseModel(BufferedReader input) throws IOException
{
+ boolean first = true;
String line = input.readLine();
- int node = 0;
while (!"//".equals(line))
{
- hmm.getNodes().add(new HMMNode());
- String next;
+ HMMNode node = new HMMNode();
+ hmm.getNodes().add(node);
Scanner matchReader = new Scanner(line);
- next = matchReader.next();
- if (next.equals(COMPO) || node > 0)
+ String next = matchReader.next();
+ if (next.equals(COMPO) || !first)
{
// stores match emission line in list
List<Double> matches = new ArrayList<>();
matches = fillList(matchReader, numberOfSymbols);
- hmm.getNodes().get(node).setMatchEmissions(matches);
- if (node > 0)
+ node.setMatchEmissions(matches);
+ if (!first)
{
- parseAnnotations(matchReader, node);
+ int column = parseAnnotations(matchReader, node);
+ hmm.setAlignmentColumn(node, column - 1);
}
}
matchReader.close();
Scanner insertReader = new Scanner(line);
List<Double> inserts = new ArrayList<>();
inserts = fillList(insertReader, numberOfSymbols);
- hmm.getNodes().get(node).setInsertEmissions(inserts);
+ node.setInsertEmissions(inserts);
insertReader.close();
// stores state transition line in list
Scanner transitionReader = new Scanner(line);
List<Double> transitions = new ArrayList<>();
transitions = fillList(transitionReader, NUMBER_OF_TRANSITIONS);
- hmm.getNodes().get(node).setStateTransitions(transitions);
+ node.setStateTransitions(transitions);
transitionReader.close();
line = input.readLine();
- node++;
- }
+ first = false;
+ }
}
/**
- * Parses the annotations on the match emission line.
+ * Parses the annotations on the match emission line and add them to the node.
+ * (See p109 of the HMMER User Guide (V3.1b2) for the specification.) Returns
+ * the alignment column number (base 1) that the node maps to, if provided,
+ * else zero.
*
* @param scanner
- * The scanner which is processing match emission line.
- * @param index
- * The index of node which is being scanned.
+ * @param node
*/
- void parseAnnotations(Scanner scanner, int index)
+ int parseAnnotations(Scanner scanner, HMMNode node)
{
+ /*
+ * map from hmm node to alignment column index, if provided
+ * HMM counts columns from 1, convert to base 0 for Jalview
+ */
+ int column = 0;
if (hmm.mapIsActive() && scanner.hasNext())
{
- int column;
column = scanner.nextInt();
- hmm.getNodes().get(index).setAlignmentColumn(column - 1);
- hmm.getNodeLookup().put(column - 1, index);
+ node.setAlignmentColumn(column - 1);
}
else
{
scanner.next();
}
+ /*
+ * hmm consensus residue if provided, else -
+ */
if (scanner.hasNext())
{
char consensusR;
consensusR = charValue(scanner.next());
- hmm.getNodes().get(index).setConsensusResidue(consensusR);
+ node.setConsensusResidue(consensusR);
}
+ /*
+ * RF reference annotation, if provided, else -
+ */
if (scanner.hasNext())
{
char reference;
reference = charValue(scanner.next());
- hmm.getNodes().get(index).setReferenceAnnotation(reference);
+ node.setReferenceAnnotation(reference);
}
+ /*
+ * 'm' for masked position, if provided, else -
+ */
if (scanner.hasNext())
{
char value;
value = charValue(scanner.next());
- hmm.getNodes().get(index).setMaskValue(value);
+ node.setMaskValue(value);
}
+
+ /*
+ * structure consensus symbol, if provided, else -
+ */
if (scanner.hasNext())
{
char consensusS;
consensusS = charValue(scanner.next());
- hmm.getNodes().get(index).setConsensusStructure(consensusS);
+ node.setConsensusStructure(consensusS);
}
- }
-
+ return column;
+ }
/**
- * Fills a list of doubles based on an input line.
+ * Fills a list of doubles from an input line
*
* @param input
* The scanner for the line containing the data to be transferred to
package jalview.hmmer;
import static org.testng.Assert.assertEquals;
-import static org.testng.Assert.assertNotEquals;
import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertTrue;
import static org.testng.Assert.fail;
import jalview.bin.Jalview;
-import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
-import jalview.io.DataSourceType;
-import jalview.io.FastaFile;
-import jalview.io.FileParse;
import jalview.ws.params.ArgumentI;
import java.io.IOException;
import java.net.MalformedURLException;
import java.util.ArrayList;
-import java.util.List;
import org.testng.annotations.AfterClass;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
-
public class HMMERTest {
AlignFrame frame;
@BeforeClass(alwaysRun = true)
- public static void setUpBeforeClass() throws Exception
+ public void setUpBeforeClass() throws Exception
{
Jalview.main(
new String[]
{ "-noquestionnaire", "-nonews", "-props",
- "test/jalview/hmmer/testProps.jvprops" });
+ "test/jalview/hmmer/testProps.jvprops", "-open",
+ "examples/uniref50.fa" });
+ // FastaFile file = null;
+ // file = new FastaFile(
+ // new FileParse("examples/uniref50.fa", DataSourceType.FILE));
+ // SequenceI[] seqs = file.getSeqsAsArray();
+ // AlignmentI al = new Alignment(seqs);
+ // frame = new AlignFrame(al, 150, 20);
+ frame = Desktop.getAlignFrames()[0];
}
@AfterClass(alwaysRun = true)
Desktop.instance.closeAll_actionPerformed(null);
}
- @Test(priority = 0)
- public void testHMMBuild() throws MalformedURLException, IOException
+ /**
+ * Test with a dependency on locally installed hmmbuild binaries
+ *
+ * @throws MalformedURLException
+ * @throws IOException
+ */
+ @Test(groups = "External")
+ public void testHMMBuildThenHMMAlign()
+ throws MalformedURLException, IOException
{
- FastaFile file = null;
- try
- {
- file = new FastaFile(
- new FileParse("examples/uniref50.fa", DataSourceType.FILE));
- } catch (IOException e)
- {
- e.printStackTrace();
- fail();
- }
- SequenceI[] seqs = file.getSeqsAsArray();
- AlignmentI al = new Alignment(seqs);
- frame = new AlignFrame(al, 150, 20);
+ /*
+ * run hmmbuild - not the side-effect of selecting the HMM
+ * sequence that gets added to the alignment
+ */
+ testHMMBuild();
+ HiddenMarkovModel hmm = frame.getSelectedHMM();
+
+ /*
+ * now run hmmalign - with respect to the select HMM profile
+ */
+ testHMMAlign();
+ }
+ public void testHMMBuild()
+ {
HMMBuildThread thread = new HMMBuildThread(frame,
new ArrayList<ArgumentI>());
thread.hmmbuildWaitTillComplete();
SequenceI seq = frame.getViewport().getAlignment().getSequenceAt(0);
HiddenMarkovModel hmm = seq.getHMM();
- if (hmm == null)
- {
- fail();
- }
+ assertNotNull(hmm);
assertEquals(hmm.getLength().intValue(), 148);
assertEquals(hmm.getAlphabetType(), "amino");
assertEquals(hmm.getConsensusAtAlignColumn(15), 's');
}
- @Test(priority = 1)
- public void testHMMAlign() throws MalformedURLException, IOException
+ public void testHMMAlign()
{
HMMAlignThread thread = new HMMAlignThread(frame,
new ArrayList<ArgumentI>());
- try
- {
- thread.hmmalignWaitTillComplete();
- } catch (Exception e)
- {
- e.printStackTrace();
- fail();
- }
+ thread.hmmalignWaitTillComplete();
- if (Desktop.getAlignFrames() == null)
+ AlignFrame[] alignFrames = Desktop.getAlignFrames();
+ if (alignFrames == null)
{
- fail();
+ fail("No align frame loaded");
}
- AlignFrame fr = Desktop.getAlignFrames()[0];
- AlignmentI al = fr.getViewport().getAlignment();
- assertNotEquals(al, null);
- List<SequenceI> hmmSeqs = al.getHMMConsensusSequences();
- assertNotNull(hmmSeqs);
+ /*
+ * now have the original align frame, and another for realigned sequences
+ */
+ assertEquals(alignFrames.length, 2);
+ AlignmentI original = alignFrames[0].getViewport().getAlignment();
+ assertNotNull(original);
+ AlignmentI realigned = alignFrames[1].getViewport().getAlignment();
+ assertNotNull(realigned);
+ assertNotNull(original.getHMMConsensusSequences());
+ assertNotNull(realigned.getHMMConsensusSequences());
+
+ SequenceI ferCapan = original.findName("FER_CAPAN");
+ assertTrue(ferCapan.getSequenceAsString().startsWith("MA------SVSAT"));
+
+ SequenceI ferCapanRealigned = realigned.findName("FER_CAPAN");
+ assertTrue(ferCapanRealigned.getSequenceAsString()
+ .startsWith("-------m-A----SVSAT"));
}
}
--- /dev/null
+#---JalviewX Properties File---
+#Fri Apr 25 09:54:25 BST 2014
+SCREEN_Y=768
+SCREEN_X=936
+SHOW_WSDISCOVERY_ERRORS=true
+LATEST_VERSION=2.8.0b1
+SHOW_CONSERVATION=true
+JALVIEW_RSS_WINDOW_SCREEN_WIDTH=550
+JAVA_CONSOLE_SCREEN_WIDTH=450
+LAST_DIRECTORY=/Volumes/Data/Users/jimp/Documents/testing/Jalview/examples
+ID_ITALICS=true
+SORT_ALIGNMENT=No sort
+SHOW_IDENTITY=true
+WSMENU_BYHOST=false
+SEQUENCE_LINKS=EMBL-EBI Search|http\://www.ebi.ac.uk/ebisearch/search.ebi?db\=allebi&query\=$SEQUENCE_ID$
+SHOW_FULLSCREEN=false
+RECENT_URL=http\://www.jalview.org/examples/exampleFile_2_7.jar
+FONT_NAME=SansSerif
+BLC_JVSUFFIX=true
+VERSION_CHECK=false
+YEAR=2011
+SHOW_DBREFS_TOOLTIP=true
+MSF_JVSUFFIX=true
+SCREENGEOMETRY_HEIGHT=1600
+JAVA_CONSOLE_SCREEN_Y=475
+JAVA_CONSOLE_SCREEN_X=830
+PFAM_JVSUFFIX=true
+PIR_JVSUFFIX=true
+STARTUP_FILE=http\://www.jalview.org/examples/exampleFile_2_3.jar
+JAVA_CONSOLE_SCREEN_HEIGHT=162
+PIR_MODELLER=false
+GAP_SYMBOL=-
+SHOW_QUALITY=true
+SHOW_OCCUPANCY=true
+SHOW_GROUP_CONSERVATION=false
+SHOW_JWS2_SERVICES=true
+SHOW_NPFEATS_TOOLTIP=true
+FONT_STYLE=plain
+ANTI_ALIAS=false
+SORT_BY_TREE=false
+RSBS_SERVICES=|Multi-Harmony|Analysis|Sequence Harmony and Multi-Relief (Brandt et al. 2010)|hseparable,gapCharacter\='-',returns\='ANNOTATION'|?tool\=jalview|http\://zeus.few.vu.nl/programs/shmrwww/index.php?tool\=jalview&groups\=$PARTITION\:min\='2',minsize\='2',sep\=' '$&ali_file\=$ALIGNMENT\:format\='FASTA',writeasfile$
+AUTHORFNAMES=Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton
+JALVIEW_RSS_WINDOW_SCREEN_HEIGHT=328
+SHOW_GROUP_CONSENSUS=false
+SHOW_CONSENSUS_HISTOGRAM=true
+SHOW_OVERVIEW=false
+AUTHORS=J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+FIGURE_AUTOIDWIDTH=false
+SCREEN_WIDTH=900
+ANNOTATIONCOLOUR_MIN=ffc800
+SHOW_STARTUP_FILE=false
+RECENT_FILE=examples/uniref50.fa\t/Volumes/Data/Users/jimp/Documents/testing/Jalview/examples/RF00031_folded.stk\t/Volumes/Data/Users/jimp/bs_ig_mult.out
+DEFAULT_FILE_FORMAT=FASTA
+SHOW_JAVA_CONSOLE=false
+VERSION=2.8b1
+FIGURE_USERIDWIDTH=
+WSMENU_BYTYPE=false
+DEFAULT_COLOUR=None
+NOQUESTIONNAIRES=true
+JALVIEW_NEWS_RSS_LASTMODIFIED=Apr 23, 2014 2\:53\:26 PM
+BUILD_DATE=01 November 2013
+PILEUP_JVSUFFIX=true
+SHOW_CONSENSUS_LOGO=false
+SCREENGEOMETRY_WIDTH=2560
+SHOW_ANNOTATIONS=true
+JALVIEW_RSS_WINDOW_SCREEN_Y=0
+USAGESTATS=false
+JALVIEW_RSS_WINDOW_SCREEN_X=0
+SHOW_UNCONSERVED=false
+SHOW_JVSUFFIX=true
+DAS_LOCAL_SOURCE=
+SCREEN_HEIGHT=650
+ANNOTATIONCOLOUR_MAX=ff0000
+AUTO_CALC_CONSENSUS=true
+FASTA_JVSUFFIX=true
+DAS_ACTIVE_SOURCE=uniprot\t
+JWS2HOSTURLS=http\://www.compbio.dundee.ac.uk/jabaws
+PAD_GAPS=false
+CLUSTAL_JVSUFFIX=true
+SHOW_ENFIN_SERVICES=true
+FONT_SIZE=10
+RIGHT_ALIGN_IDS=false
+USE_PROXY=false
+WRAP_ALIGNMENT=false
+#DAS_REGISTRY_URL=http\://www.dasregistry.org/das/ # retired 01/05/2015
+DAS_REGISTRY_URL=http\://www.ebi.ac.uk/das-srv/registry/das/
+logs.Jalview.level=DEBUG
+HMMER_PATH=/Users/gmcarstairs/software/hmmer-3.1b2-macosx-intel/binaries
import java.io.IOException;
import java.io.PrintWriter;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.List;
import java.util.Scanner;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class HMMFileTest {
+ HMMFile fn3;
+ HMMFile pKinase;
- HMMFile fn3 = new HMMFile(new BufferedReader(
- new FileReader(("test/jalview/io/test_fn3_hmm.txt"))));
+ HMMFile made1;
- HMMFile pKinase = new HMMFile(new BufferedReader(
- new FileReader(("test/jalview/io/test_PKinase_hmm.txt"))));
-
- HMMFile made1 = new HMMFile(new BufferedReader(
- new FileReader(("test/jalview/io/test_MADE1_hmm.txt"))));
-
- HMMFileTest() throws IOException
+ @BeforeClass(alwaysRun = true)
+ public void setUp() throws FileNotFoundException
{
+ fn3 = new HMMFile(new BufferedReader(
+ new FileReader(("test/jalview/io/test_fn3_hmm.txt"))));
- }
-
-
+ pKinase = new HMMFile(new BufferedReader(
+ new FileReader(("test/jalview/io/test_PKinase_hmm.txt"))));
+ made1 = new HMMFile(new BufferedReader(
+ new FileReader(("test/jalview/io/test_MADE1_hmm.txt"))));
+ }
- @Test
+ @Test(groups = "Functional")
public void testParse() throws IOException
{
-
pKinase.parse();
HiddenMarkovModel hmm = pKinase.getHMM();
assertEquals(hmm.getName(), "Pkinase");
assertEquals(hmm.getTrustedCutoff(), "70.30 70.30");
assertEquals(hmm.getNoiseCutoff(), "70.20 70.20");
- List<Character> symbols = new ArrayList<>();
- symbols.add('A');
- symbols.add('C');
- symbols.add('D');
- symbols.add('E');
- symbols.add('F');
- symbols.add('G');
- symbols.add('H');
- symbols.add('I');
- symbols.add('K');
- symbols.add('L');
- symbols.add('M');
- symbols.add('N');
- symbols.add('P');
- symbols.add('Q');
- symbols.add('R');
- symbols.add('S');
- symbols.add('T');
- symbols.add('V');
- symbols.add('W');
- symbols.add('Y');
-
+ List<Character> symbols = Arrays
+ .asList(new Character[]
+ { 'A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N',
+ 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y' });
assertEquals(hmm.getSymbols(), symbols);
assertEquals(hmm.getMatchEmissionProbability(0, 'Y'), 0.16102, 0.001d);
public void testParseAnnotations()
{
HMMFile testFile = new HMMFile();
- testFile.setHMM(new HiddenMarkovModel());
- testFile.getHMM().getNodes().add(new HMMNode());
- testFile.getHMM().getNodes().add(new HMMNode());
- testFile.getHMM().getNodes().add(new HMMNode());
-
-
- testFile.getHMM().setConsensusResidueStatus(true);
- testFile.getHMM().setMAPStatus(true);
- testFile.getHMM().setReferenceAnnotationStatus(true);
- testFile.getHMM().setConsensusStructureStatus(true);
- testFile.getHMM().setMaskedValueStatus(true);
+ HiddenMarkovModel hmm = new HiddenMarkovModel();
+ testFile.setHMM(hmm);
+ hmm.getNodes().add(new HMMNode());
+
+ hmm.setConsensusResidueStatus(true);
+ hmm.setMAPStatus(true);
+ hmm.setReferenceAnnotationStatus(true);
+ hmm.setConsensusStructureStatus(true);
+ hmm.setMaskedValueStatus(true);
Scanner scanner = new Scanner("1345 t t t t");
- testFile.parseAnnotations(scanner, 1);
-
- testFile.getHMM().setConsensusResidueStatus(true);
- testFile.getHMM().setMAPStatus(false);
- testFile.getHMM().setReferenceAnnotationStatus(true);
- testFile.getHMM().setConsensusStructureStatus(false);
- testFile.getHMM().setMaskedValueStatus(false);
+ HMMNode node = new HMMNode();
+ hmm.getNodes().add(node);
+ testFile.parseAnnotations(scanner, node);
+
+ hmm.setConsensusResidueStatus(true);
+ hmm.setMAPStatus(false);
+ hmm.setReferenceAnnotationStatus(true);
+ hmm.setConsensusStructureStatus(false);
+ hmm.setMaskedValueStatus(false);
Scanner scanner2 = new Scanner("- y x - -");
- testFile.parseAnnotations(scanner2, 2);
-
- HiddenMarkovModel hmm = testFile.getHMM();
+ node = new HMMNode();
+ hmm.getNodes().add(node);
+ testFile.parseAnnotations(scanner2, node);
assertEquals(hmm.getNodeAlignmentColumn(1).intValue(), 1344);
assertEquals(hmm.getConsensusResidue(1), 't');
assertEquals(hmm.getMaskedValue(1), 't');
assertEquals(hmm.getConsensusStructure(1), 't');
- assertEquals(hmm.findNodeIndex(1344).intValue(), 1);
-
scanner.close();
-
}
/**
git://source.jalview.org / jalview.git / commitdiff