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Resource update #8

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8176ba9
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JuliansGHUB1 Jan 9, 2024
50aac8a
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JuliansGHUB1 Jan 9, 2024
474d29f
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JuliansGHUB1 Jan 9, 2024
7cc6e74
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JuliansGHUB1 Jan 9, 2024
151f67b
updates to resource
JuliansGHUB1 Jan 9, 2024
adce421
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JuliansGHUB1 Jan 9, 2024
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1 change: 1 addition & 0 deletions .gitignore
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target/
56 changes: 56 additions & 0 deletions resource.iml
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<?xml version="1.0" encoding="UTF-8"?>
<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
<component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_8">
<output url="file://$MODULE_DIR$/target/classes" />
<output-test url="file://$MODULE_DIR$/target/test-classes" />
<content url="file://$MODULE_DIR$">
<sourceFolder url="file://$MODULE_DIR$/src/main/java" isTestSource="false" />
<sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
<excludeFolder url="file://$MODULE_DIR$/target" />
</content>
<orderEntry type="inheritedJdk" />
<orderEntry type="sourceFolder" forTests="false" />
<orderEntry type="library" scope="TEST" name="Maven: junit:junit:4.13.2" level="project" />
<orderEntry type="library" scope="TEST" name="Maven: org.hamcrest:hamcrest-core:1.3" level="project" />
<orderEntry type="library" name="Maven: org.panda:utility:1.2.1-SNAPSHOT" level="project" />
<orderEntry type="library" name="Maven: org.apache.commons:commons-math3:3.3" level="project" />
<orderEntry type="library" name="Maven: org.apache.commons:commons-compress:1.7" level="project" />
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<orderEntry type="library" name="Maven: com.github.fommil.netlib:netlib-native_system-win-i686:natives:1.1" level="project" />
<orderEntry type="library" name="Maven: org.jetbrains:annotations:24.1.0" level="project" />
<orderEntry type="library" name="Maven: org.biopax.paxtools:paxtools-core:5.1.0" level="project" />
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</component>
</module>
22 changes: 21 additions & 1 deletion src/main/java/org/panda/resource/UniProtSequence.java
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Expand Up @@ -5,6 +5,7 @@

package org.panda.resource;


import java.io.BufferedReader;
import java.io.IOException;
import java.util.HashMap;
Expand Down Expand Up @@ -129,6 +130,19 @@ public String getSeqAround(String idOrName, int prefixLen, int suffixLen, int lo
*/
int max = ((prefixLen > suffixLen ? prefixLen : suffixLen) * 2) + 1;



// max/2 is how many you want to left/right of central position
// if you want k to the right, and you are at the kth position or lesser, this is impossible
if(max/2 >= location){
return null;
}

/*
The call to getSeqAround takes the width as an argument. Consider, if the width/2 = k,
then there will be k amino acids to the left and to the right.
*/

// Will take an odd-length as argument, and return sequence of that length
// centered around location

Expand Down Expand Up @@ -189,7 +203,11 @@ public boolean load() throws IOException {
this.nameToID.put(name, id);
sequence = new StringBuilder();
int oInd = line.indexOf(" OX=");
String organism = line.substring(oInd + 4, line.indexOf(" ", oInd + 4));


String organism = line. substring(oInd + 4, line.indexOf(" ", oInd + 4));


int sInd = line.indexOf(" GN=");
if (sInd > 0) {
String symbol = line.substring(sInd + 4, line.indexOf(" ", sInd + 4));
Expand All @@ -202,9 +220,11 @@ public boolean load() throws IOException {
}
} else {
sequence.append(line);

}
}


reader.close();
return true;
}
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