From 9a004c9c9166ab52f58dcdd9463292956d98dce4 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Mon, 16 Nov 2009 15:38:27 +0000
Subject: [PATCH] SE-163
SVN: 13426
---
.../phosphonetx/BuildAndEnvironmentInfo.java | 46 ------
.../client/application/OccurrencesMarker.java | 148 +-----------------
.../shared/basic/dto/Occurrence.java | 64 ++++++++
.../shared/basic/dto/OccurrenceUtil.java | 84 ++++++++++
.../application/OccurrencesMarkerTest.java | 4 +-
.../shared/basic/dto/OccurrenceUtilTest.java | 46 ++++++
6 files changed, 200 insertions(+), 192 deletions(-)
delete mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/BuildAndEnvironmentInfo.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/Occurrence.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/OccurrenceUtil.java
create mode 100644 rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/OccurrenceUtilTest.java
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/BuildAndEnvironmentInfo.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/BuildAndEnvironmentInfo.java
deleted file mode 100644
index 3cfcbdfbfd9..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/BuildAndEnvironmentInfo.java
+++ /dev/null
@@ -1,46 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.phosphonetx;
-
-import ch.systemsx.cisd.base.utilities.AbstractBuildAndEnvironmentInfo;
-
-
-/**
- * The build and environment information for PhosphoNetX.
- *
- * @author Franz-Josef Elmer
- */
-public class BuildAndEnvironmentInfo extends AbstractBuildAndEnvironmentInfo
-{
- private final static String BASE = "rtd_phosphonetx";
-
- public final static BuildAndEnvironmentInfo INSTANCE = new BuildAndEnvironmentInfo();
-
- private BuildAndEnvironmentInfo()
- {
- super(BASE);
- }
-
- /**
- * Shows build and environment information on the console.
- */
- public static void main(String[] args)
- {
- System.out.println(INSTANCE);
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/OccurrencesMarker.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/OccurrencesMarker.java
index 006bd2f2cf2..87cd57b8d6c 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/OccurrencesMarker.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/OccurrencesMarker.java
@@ -16,10 +16,11 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application;
-import java.util.ArrayList;
-import java.util.Collections;
import java.util.List;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.Occurrence;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.OccurrenceUtil;
+
/**
* This class is able to find all occurrences of the given set of words in the provided template and
* mark the beginning and end of those words. Note that when occurrences overlap the overlaps are
@@ -135,105 +136,7 @@ public class OccurrencesMarker
*/
public String mark(String template, List<String> words)
{
- List<Occurrence> occurrences = calcSortedOccurrences(template, words);
- if (hasOverlapping(occurrences))
- {
- return markOverlapping(template, occurrences);
- } else
- {
- return markNonoverlapping(template, occurrences);
- }
- }
-
- // describes one occurence of the word in a template
- private static class Occurrence implements Comparable<Occurrence>
- {
- private final String word;
-
- private final int startIndex;
-
- public Occurrence(String word, int startIndex)
- {
- this.word = word;
- this.startIndex = startIndex;
- }
-
- public String getWord()
- {
- return word;
- }
-
- public int getStartIndex()
- {
- return startIndex;
- }
-
- public int getEndIndex()
- {
- return startIndex + word.length() - 1;
- }
-
- public int compareTo(Occurrence o)
- {
- return getStartIndex() - o.getStartIndex();
- }
-
- @Override
- public String toString()
- {
- return "[" + word + "@" + startIndex + "]";
- }
- }
-
- private String markOverlapping(String template, List<Occurrence> sortedOccurrences)
- {
- List<Occurrence> mergedOccurrences = mergeOverlaps(template, sortedOccurrences);
- return markNonoverlapping(template, mergedOccurrences);
- }
-
- private List<Occurrence> mergeOverlaps(String template, List<Occurrence> sortedOccurrences)
- {
- List<Occurrence> result = new ArrayList<Occurrence>();
- if (sortedOccurrences.size() == 0)
- {
- return result;
- }
- int startIndex = -1;
- int endIndex = -1;
- for (Occurrence occurrence : sortedOccurrences)
- {
- if (occurrence.getStartIndex() <= endIndex)
- { // overlap
- endIndex = Math.max(endIndex, occurrence.getEndIndex());
- } else
- { // current word does not overlap with the words browsed before
- if (startIndex != -1)
- { // create a new word from the words browsed before
- Occurrence newOccurrence = createOccurence(template, startIndex, endIndex);
- result.add(newOccurrence);
- }
- startIndex = occurrence.getStartIndex();
- endIndex = occurrence.getEndIndex();
- }
- }
- Occurrence newOccurrence = createOccurence(template, startIndex, endIndex);
- result.add(newOccurrence);
- return result;
- }
-
- private static Occurrence createOccurence(String template, int startIndex, int endIndex)
- {
- assert startIndex != -1 : "start index should be initialized";
- assert endIndex != -1 : "end index should be initialized";
- String mergedWord = template.substring(startIndex, endIndex + 1);
- Occurrence newOccurrence = new Occurrence(mergedWord, startIndex);
- return newOccurrence;
- }
-
- // marks all occurrences in the template, assuming that all occurrences do not
- // overlap with each other and are sorted by the start position
- private String markNonoverlapping(String template, List<Occurrence> sortedOccurrences)
- {
+ List<Occurrence> sortedOccurrences = OccurrenceUtil.getCoverage(template, words);
StringBuffer sb = new StringBuffer();
int nextUnprocessedCharIndex = 0;
for (Occurrence occurrence : sortedOccurrences)
@@ -249,47 +152,4 @@ public class OccurrencesMarker
return sb.toString();
}
- // true if two occurrences of the same word in the template overlap (have a common part)
- private static boolean hasOverlapping(List<Occurrence> occurrences)
- {
- int prevEndIndex = -1;
- for (Occurrence occurrence : occurrences)
- {
- if (occurrence.getStartIndex() <= prevEndIndex)
- {
- return true;
- }
- prevEndIndex = Math.max(prevEndIndex, occurrence.getEndIndex());
- }
- return false;
- }
-
- // calculates a list of all words occurances, sorts it be starting position
- private static List<Occurrence> calcSortedOccurrences(String template, List<String> words)
- {
- List<Occurrence> result = new ArrayList<Occurrence>();
- for (String word : words)
- {
- result.addAll(calcOccurrences(template, word));
- }
- Collections.sort(result);
- return result;
- }
-
- private static List<Occurrence> calcOccurrences(String template, String word)
- {
- List<Occurrence> result = new ArrayList<Occurrence>();
- int startIndex = 0;
- while (true)
- {
- int occurrenceIndex = template.indexOf(word, startIndex);
- if (occurrenceIndex == -1)
- {
- break;
- }
- result.add(new Occurrence(word, occurrenceIndex));
- startIndex = occurrenceIndex + 1; // maybe the word overlaps with itself?
- }
- return result;
- }
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/Occurrence.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/Occurrence.java
new file mode 100644
index 00000000000..0a79583f908
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/Occurrence.java
@@ -0,0 +1,64 @@
+/*
+ * Copyright 2009 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto;
+
+/**
+ * The occurrence of a word in a text. Occurrences are comparable by their start indexes.
+ *
+ * @author Tomasz Pylak
+ */
+public class Occurrence implements Comparable<Occurrence>
+{
+ private final String word;
+
+ private final int startIndex;
+
+ /**
+ * Creates a new instance of the specified word which appears at the specified start index.
+ */
+ public Occurrence(String word, int startIndex)
+ {
+ this.word = word;
+ this.startIndex = startIndex;
+ }
+
+ public String getWord()
+ {
+ return word;
+ }
+
+ public int getStartIndex()
+ {
+ return startIndex;
+ }
+
+ public int getEndIndex()
+ {
+ return startIndex + word.length() - 1;
+ }
+
+ public int compareTo(Occurrence o)
+ {
+ return getStartIndex() - o.getStartIndex();
+ }
+
+ @Override
+ public String toString()
+ {
+ return "[" + word + "@" + startIndex + "]";
+ }
+}
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/OccurrenceUtil.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/OccurrenceUtil.java
new file mode 100644
index 00000000000..a9564e33dee
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/OccurrenceUtil.java
@@ -0,0 +1,84 @@
+/*
+ * Copyright 2009 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+
+/**
+ * Helper class for calculating peptide on protein coverage.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class OccurrenceUtil
+{
+ /**
+ * Returns a list of non-overlapping sequences built by the specified peptides covering the
+ * specified protein.
+ */
+ public static List<Occurrence> getCoverage(String protein, List<String> peptides)
+ {
+ ArrayList<Occurrence> list = new ArrayList<Occurrence>();
+ List<Occurrence> sortedList = calcSortedOccurrences(protein, peptides);
+ if (sortedList.isEmpty() == false)
+ {
+ Occurrence current = sortedList.get(0);
+ for (int i = 1; i < sortedList.size(); i++)
+ {
+ String currentPeptide = current.getWord();
+ Occurrence next = sortedList.get(i);
+ int diff = next.getStartIndex() - current.getStartIndex();
+ if (current.getWord().length() < diff)
+ {
+ list.add(current);
+ current = next;
+ } else if (current.getEndIndex() < next.getEndIndex())
+ {
+ String mergedPeptides = currentPeptide.substring(0, diff) + next.getWord();
+ current = new Occurrence(mergedPeptides, current.getStartIndex());
+ }
+ }
+ list.add(current);
+ }
+ return list;
+ }
+
+ // calculates a list of all words occurences, sorts it be starting position
+ private static List<Occurrence> calcSortedOccurrences(String protein, List<String> peptides)
+ {
+ List<Occurrence> result = new ArrayList<Occurrence>();
+ for (String word : peptides)
+ {
+ int startIndex = 0;
+ while (true)
+ {
+ int occurrenceIndex = protein.indexOf(word, startIndex);
+ if (occurrenceIndex == -1)
+ {
+ break;
+ }
+ result.add(new Occurrence(word, occurrenceIndex));
+ startIndex = occurrenceIndex + 1; // maybe the word overlaps with itself?
+ }
+ }
+ Collections.sort(result);
+ return result;
+ }
+
+}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/OccurrencesMarkerTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/OccurrencesMarkerTest.java
index 3679c81b71d..84aefd07bd0 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/OccurrencesMarkerTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/OccurrencesMarkerTest.java
@@ -46,8 +46,8 @@ public class OccurrencesMarkerTest extends AssertJUnit
public void testFindOverlappingOccurrences()
{
OccurrencesMarker marker = createMarker();
- String marked = marker.mark("aaaa", Arrays.asList("aa"));
- assertEquals("<aaaa>", marked);
+ assertEquals("<aaaa>", marker.mark("aaaa", Arrays.asList("aa")));
+ assertEquals("h<ello> w<orld>, h<ello> universe!", marker.mark("hello world, hello universe!", Arrays.asList("ell", "o", "orld")));
}
@Test
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/OccurrenceUtilTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/OccurrenceUtilTest.java
new file mode 100644
index 00000000000..0b14def68ad
--- /dev/null
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/OccurrenceUtilTest.java
@@ -0,0 +1,46 @@
+/*
+ * Copyright 2009 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto;
+
+import java.util.Arrays;
+
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class OccurrenceUtilTest extends AssertJUnit
+{
+ @Test
+ public void test()
+ {
+ check("[[ab@0], [abcd@4], [ab@13]]", "abc abcde hahab", "ab", "bcd");
+ check("[[ab@0], [abcd@4], [ab@13]]", "abc abcde hahab", "ab", "cd");
+ check("[[abc@0], [abc@4], [ab@13]]", "abc abcde hahab", "ab", "b", "c");
+ check("[[abc@0], [abc@4], [b@14]]", "abc abcde hahab", "abc", "b");
+ check("[[abcde@0]]", "abcdef", "abcd", "b", "de");
+ check("[[haha@10]]", "abc abcde hahab", "haha", "h");
+ }
+
+ private void check(String expectedList, String sequence, String... words)
+ {
+ assertEquals(expectedList, OccurrenceUtil.getCoverage(sequence, Arrays.asList(words)).toString());
+ }
+}
--
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