| @@ -1,4 +1,43 @@ |
| <?xml version="1.0" encoding="UTF-8"?> |
| +<!-- |
| +DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER. |
| + |
| +Copyright (c) 2006, 2016 Oracle and/or its affiliates. All rights reserved. |
| + |
| +Oracle and Java are registered trademarks of Oracle and/or its affiliates. |
| +Other names may be trademarks of their respective owners. |
| + |
| +The contents of this file are subject to the terms of either the GNU |
| +General Public License Version 2 only ("GPL") or the Common |
| +Development and Distribution License("CDDL") (collectively, the |
| +"License"). You may not use this file except in compliance with the |
| +License. You can obtain a copy of the License at |
| +http://www.netbeans.org/cddl-gplv2.html |
| +or nbbuild/licenses/CDDL-GPL-2-CP. See the License for the |
| +specific language governing permissions and limitations under the |
| +License. When distributing the software, include this License Header |
| +Notice in each file and include the License file at |
| +nbbuild/licenses/CDDL-GPL-2-CP. Oracle designates this |
| +particular file as subject to the "Classpath" exception as provided |
| +by Oracle in the GPL Version 2 section of the License file that |
| +accompanied this code. If applicable, add the following below the |
| +License Header, with the fields enclosed by brackets [] replaced by |
| +your own identifying information: |
| +"Portions Copyrighted [year] [name of copyright owner]" |
| + |
| +If you wish your version of this file to be governed by only the CDDL |
| +or only the GPL Version 2, indicate your decision by adding |
| +"[Contributor] elects to include this software in this distribution |
| +under the [CDDL or GPL Version 2] license." If you do not indicate a |
| +single choice of license, a recipient has the option to distribute |
| +your version of this file under either the CDDL, the GPL Version 2 or |
| +to extend the choice of license to its licensees as provided above. |
| +However, if you add GPL Version 2 code and therefore, elected the GPL |
| +Version 2 license, then the option applies only if the new code is |
| +made subject to such option by the copyright holder. |
| + |
| +Contributor(s): |
| +--> |
| <project default="-deploy-ant" basedir="."> |
| <target name="-init" if="deploy.ant.enabled"> |
| <property file="${deploy.ant.properties.file}"/> |
| @@ -16,7 +55,7 @@ |
| <isset property="tomcat.password"/> |
| </not> |
| </condition> |
| - </fail> |
| + </fail> |
| </target> |
| <target name="-deploy-ant" if="deploy.ant.enabled" depends="-init,-check-credentials"> |
| <echo message="Deploying ${deploy.ant.archive} to ${Context(path)}"/> |
| @@ -1009,9 +1009,9 @@ |
| <copyfiles files="${libs.CSIP-Jersey-2.16.classpath}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/> |
| <copyfiles files="${reference.csip-core.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/> |
| <copyfiles files="${file.reference.commons-math-2.0.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/> |
| - <copyfiles files="${file.reference.Jama-1.0.2.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/> |
| <copyfiles files="${file.reference.jcommon-1.0.16.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/> |
| <copyfiles files="${file.reference.jfreechart-1.0.13.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/> |
| + <copyfiles files="${file.reference.Jama-1.0.2.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/> |
| <mkdir dir="${build.web.dir}/META-INF"/> |
| <manifest file="${build.web.dir}/META-INF/MANIFEST.MF" mode="update"/> |
| </target> |
| @@ -1019,9 +1019,9 @@ |
| <copyfiles files="${libs.CSIP-Jersey-2.16.classpath}" todir="${build.web.dir}/WEB-INF/lib"/> |
| <copyfiles files="${reference.csip-core.jar}" todir="${build.web.dir}/WEB-INF/lib"/> |
| <copyfiles files="${file.reference.commons-math-2.0.jar}" todir="${build.web.dir}/WEB-INF/lib"/> |
| - <copyfiles files="${file.reference.Jama-1.0.2.jar}" todir="${build.web.dir}/WEB-INF/lib"/> |
| <copyfiles files="${file.reference.jcommon-1.0.16.jar}" todir="${build.web.dir}/WEB-INF/lib"/> |
| <copyfiles files="${file.reference.jfreechart-1.0.13.jar}" todir="${build.web.dir}/WEB-INF/lib"/> |
| + <copyfiles files="${file.reference.Jama-1.0.2.jar}" todir="${build.web.dir}/WEB-INF/lib"/> |
| </target> |
| <target depends="init" if="dist.ear.dir" name="-clean-webinf-lib"> |
| <delete dir="${build.web.dir}/WEB-INF/lib"/> |
| @@ -1,3 +1,5 @@ |
| +file.reference.Jama-1.0.2.jar=lib/Jama-1.0.2.jar |
| +j2ee.platform.classpath=${j2ee.server.home}/lib/annotations-api.jar:${j2ee.server.home}/lib/catalina-ant.jar:${j2ee.server.home}/lib/catalina-ha.jar:${j2ee.server.home}/lib/catalina-storeconfig.jar:${j2ee.server.home}/lib/catalina-tribes.jar:${j2ee.server.home}/lib/catalina.jar:${j2ee.server.home}/lib/ecj-4.4.2.jar:${j2ee.server.home}/lib/el-api.jar:${j2ee.server.home}/lib/jasper-el.jar:${j2ee.server.home}/lib/jasper.jar:${j2ee.server.home}/lib/jsp-api.jar:${j2ee.server.home}/lib/servlet-api.jar:${j2ee.server.home}/lib/tomcat-api.jar:${j2ee.server.home}/lib/tomcat-coyote.jar:${j2ee.server.home}/lib/tomcat-dbcp.jar:${j2ee.server.home}/lib/tomcat-i18n-es.jar:${j2ee.server.home}/lib/tomcat-i18n-fr.jar:${j2ee.server.home}/lib/tomcat-i18n-ja.jar:${j2ee.server.home}/lib/tomcat-jdbc.jar:${j2ee.server.home}/lib/tomcat-jni.jar:${j2ee.server.home}/lib/tomcat-util-scan.jar:${j2ee.server.home}/lib/tomcat-util.jar:${j2ee.server.home}/lib/tomcat-websocket.jar:${j2ee.server.home}/lib/websocket-api.jar |
| #Fri May 06 09:05:19 MDT 2016 |
| javadoc.splitindex=true |
| lib.dir=${web.docbase.dir}/WEB-INF/lib |
| @@ -11,7 +13,6 @@ |
| build.web.excludes=${build.classes.excludes} |
| war.ear.name=${war.name} |
| j2ee.compile.on.save=true |
| -j2ee.platform.classpath=${j2ee.server.home}/lib/annotations-api.jar\:${j2ee.server.home}/lib/catalina-ant.jar\:${j2ee.server.home}/lib/catalina-ha.jar\:${j2ee.server.home}/lib/catalina-storeconfig.jar\:${j2ee.server.home}/lib/catalina-tribes.jar\:${j2ee.server.home}/lib/catalina.jar\:${j2ee.server.home}/lib/ecj-4.4.2.jar\:${j2ee.server.home}/lib/el-api.jar\:${j2ee.server.home}/lib/jasper-el.jar\:${j2ee.server.home}/lib/jasper.jar\:${j2ee.server.home}/lib/jsp-api.jar\:${j2ee.server.home}/lib/servlet-api.jar\:${j2ee.server.home}/lib/tomcat-api.jar\:${j2ee.server.home}/lib/tomcat-coyote.jar\:${j2ee.server.home}/lib/tomcat-dbcp.jar\:${j2ee.server.home}/lib/tomcat-i18n-es.jar\:${j2ee.server.home}/lib/tomcat-i18n-fr.jar\:${j2ee.server.home}/lib/tomcat-i18n-ja.jar\:${j2ee.server.home}/lib/tomcat-jdbc.jar\:${j2ee.server.home}/lib/tomcat-jni.jar\:${j2ee.server.home}/lib/tomcat-util-scan.jar\:${j2ee.server.home}/lib/tomcat-util.jar\:${j2ee.server.home}/lib/tomcat-websocket.jar\:${j2ee.server.home}/lib/websocket-api.jar |
| debug.test.classpath=${run.test.classpath} |
| build.dir=build |
| javac.deprecation=false |
| @@ -30,7 +31,9 @@ |
| javac.source=1.8 |
| javac.debug=true |
| javac.test.processorpath=${javac.test.classpath} |
| -run.test.classpath=${javac.test.classpath}\:${build.test.classes.dir} |
| +run.test.classpath=\ |
| + ${javac.test.classpath}:\ |
| + ${build.test.classes.dir} |
| build.generated.sources.dir=${build.dir}/generated-sources |
| javadoc.notree=false |
| runmain.jvmargs= |
| @@ -41,10 +44,15 @@ |
| annotation.processing.enabled=true |
| war.content.additional= |
| dist.javadoc.dir=${dist.dir}/javadoc |
| -file.reference.Jama-1.0.2.jar=lib/Jama-1.0.2.jar |
| client.urlPart= |
| javadoc.additionalparam= |
| -javac.classpath=${libs.CSIP-Jersey-2.16.classpath}\:${reference.csip-core.jar}\:${file.reference.commons-math-2.0.jar}\:${file.reference.Jama-1.0.2.jar}\:${file.reference.jcommon-1.0.16.jar}\:${file.reference.jfreechart-1.0.13.jar} |
| +javac.classpath=\ |
| + ${libs.CSIP-Jersey-2.16.classpath}:\ |
| + ${reference.csip-core.jar}:\ |
| + ${file.reference.commons-math-2.0.jar}:\ |
| + ${file.reference.jcommon-1.0.16.jar}:\ |
| + ${file.reference.jfreechart-1.0.13.jar}:\ |
| + ${file.reference.Jama-1.0.2.jar} |
| javadoc.noindex=false |
| webinf.dir=web/WEB-INF |
| annotation.processing.enabled.in.editor=true |
| @@ -63,10 +71,12 @@ |
| annotation.processing.run.all.processors=true |
| compile.jsps=false |
| excludes= |
| -javac.processorpath=${javac.classpath} |
| +javac.processorpath=\ |
| + ${javac.classpath} |
| build.test.results.dir=${build.dir}/test/results |
| display.browser=false |
| -endorsed.classpath=${libs.javaee-endorsed-api-6.0.classpath} |
| +endorsed.classpath=\ |
| + ${libs.javaee-endorsed-api-6.0.classpath} |
| javadoc.use=true |
| build.web.dir=${build.dir}/web |
| javadoc.nonavbar=false |
| @@ -24,10 +24,6 @@ |
| <path-in-war>WEB-INF/lib</path-in-war> |
| </library> |
| <library dirs="200"> |
| - <file>${file.reference.Jama-1.0.2.jar}</file> |
| - <path-in-war>WEB-INF/lib</path-in-war> |
| - </library> |
| - <library dirs="200"> |
| <file>${file.reference.jcommon-1.0.16.jar}</file> |
| <path-in-war>WEB-INF/lib</path-in-war> |
| </library> |
| @@ -35,6 +31,10 @@ |
| <file>${file.reference.jfreechart-1.0.13.jar}</file> |
| <path-in-war>WEB-INF/lib</path-in-war> |
| </library> |
| + <library dirs="200"> |
| + <file>${file.reference.Jama-1.0.2.jar}</file> |
| + <path-in-war>WEB-INF/lib</path-in-war> |
| + </library> |
| </web-module-libraries> |
| <web-module-additional-libraries/> |
| <source-roots> |
| @@ -127,10 +127,10 @@ |
| * @throws ParseException |
| */ |
| public double[] CDPHE_Biological(String[][] flowData, |
| - int m, |
| - int R, |
| - int clusterLength, |
| - int clusterCountMax) throws IOException, ParseException{ |
| + int m, |
| + int R, |
| + int clusterLength, |
| + int clusterCountMax) throws IOException, ParseException{ |
| //Calculate annual design low flow |
| double DFLOW_annual = CDPHE_Biological_calcs(flowData, m, R, clusterLength, clusterCountMax); |
| |
| @@ -202,10 +202,10 @@ |
| * @throws ParseException |
| */ |
| private double CDPHE_Biological_calcs(String[][] flowData, |
| - int m, |
| - int R, |
| - int clusterLength, |
| - int clusterCountMax) throws IOException, ParseException{ |
| + int m, |
| + int R, |
| + int clusterLength, |
| + int clusterCountMax) throws IOException, ParseException{ |
| //Calculate m-day statistics |
| Object[] resultArray = DoubleArray.getMdayData(flowData, m, "harmonic"); |
| ArrayList<String> average_Mday_date = (ArrayList<String>) resultArray[0]; |
| @@ -213,6 +213,10 @@ |
| |
| //Get extreme-value based design flow (as a trial design flow to start searching for the biologically based one, note this still uses an arithmetic mean) |
| double trialDFLOW = CDPHE_ExtremeValue(flowData, m, R, "04-01"); |
| + if(trialDFLOW == 0){ |
| + //Catch zero-flow guess to avoid ending the convergence loop early and reporting a zero when it shouldn't be zero |
| + trialDFLOW = DoubleMath.meanHarmonic(average_Mday); |
| + } |
| double trialDFLOW_excursions = countExcursions(average_Mday_date, average_Mday, m, trialDFLOW, clusterLength, clusterCountMax); |
| |
| //Get allowed number of excursions |
| @@ -253,10 +257,6 @@ |
| } |
| ctr++; |
| } |
| - |
| - //Call file writer for outputs fo flow statistics |
| - designFlow = DoubleMath.round(designFlow, 3); |
| - |
| return designFlow; |
| } |
| /** |
| @@ -527,7 +527,7 @@ |
| median_R_yearFlow = DoubleMath.round(median_R_yearFlow, 2); |
| |
| //Format the results into a summary table |
| - String summaryTable = "Month\t1E3 Acute Monthly Low Flows\t7E3 Chronic Monthly Low Flows\t30E3 Chronic Monthly Low Flows"; |
| + String summaryTable = "Month\t1E3 Acute Monthly Low Flows [cfs]\t7E3 Chronic Monthly Low Flows [cfs]\t30E3 Chronic Monthly Low Flows [cfs]"; |
| String[] months = {"Entire Record", "January", "February", "March", "April", "May", "June", "July", "August", "September", "October", "November", "December", "Lowest Monthly Flow"}; |
| for(int i=0; i<13; i++){ |
| summaryTable = summaryTable + "\r\n" + months[i] + "\t" + monthlyBiological_1day[i] + "\t" + monthlyBiological_7day[i] + "\t" + monthlyBiological_30day[i]; |