Initial commit

bibliography.bib

@@ -0,0 +1,320 @@
+@article{guha1998approximation,
+  title={Approximation algorithms for connected dominating sets},
+  author={Guha, Sudipto and Khuller, Samir},
+  journal={Algorithmica},
+  volume={20},
+  number={4},
+  pages={374--387},
+  year={1998},
+  publisher={Springer}
+}
+
+@article{chan2012approximation,
+  title={Approximation algorithms for maximum independent set of pseudo-disks},
+  author={Chan, Timothy M and Har-Peled, Sariel},
+  journal={Discrete \& Computational Geometry},
+  volume={48},
+  number={2},
+  pages={373--392},
+  year={2012},
+  publisher={Springer}
+}
+
+@article{erlebach2005polynomial,
+  title={Polynomial-time approximation schemes for geometric intersection graphs},
+  author={Erlebach, Thomas and Jansen, Klaus and Seidel, Eike},
+  journal={SIAM Journal on Computing},
+  volume={34},
+  number={6},
+  pages={1302--1323},
+  year={2005},
+  publisher={SIAM}
+}
+
+@article{bafna1996nonoverlapping,
+  title={Nonoverlapping local alignments (weighted independent sets of axis-parallel rectangles)},
+  author={Bafna, Vineet and Narayanan, Babu and Ravi, R},
+  journal={Discrete Applied Mathematics},
+  volume={71},
+  number={1-3},
+  pages={41--53},
+  year={1996},
+  publisher={Elsevier}
+}
+
+@article{chandra2001greedy,
+  title={Greedy local improvement and weighted set packing approximation},
+  author={Chandra, Barun and Halld{\'o}rsson, Magn{\'u}s M},
+  journal={Journal of Algorithms},
+  volume={39},
+  number={2},
+  pages={223--240},
+  year={2001},
+  publisher={Elsevier}
+}
+
+@inproceedings{berman2000d,
+  title={A d/2 approximation for maximum weight independent set in d-claw free graphs},
+  author={Berman, Piotr},
+  booktitle={Scandinavian Workshop on Algorithm Theory},
+  pages={214--219},
+  year={2000},
+  organization={Springer}
+}
+
+@article{newman2004fast,
+  title={Fast algorithm for detecting community structure in networks},
+  author={Newman, Mark EJ},
+  journal={Physical review E},
+  volume={69},
+  number={6},
+  pages={066133},
+  year={2004},
+  publisher={APS}
+}
+
+@article{clauset2004finding,
+  title={Finding community structure in very large networks},
+  author={Clauset, Aaron and Newman, Mark EJ and Moore, Cristopher},
+  journal={Physical review E},
+  volume={70},
+  number={6},
+  pages={066111},
+  year={2004},
+  publisher={APS}
+}
+
+@article{blondel2008fast,
+  title={Fast unfolding of communities in large networks},
+  author={Blondel, Vincent D and Guillaume, Jean-Loup and Lambiotte, Renaud and Lefebvre, Etienne},
+  journal={Journal of statistical mechanics: theory and experiment},
+  volume={2008},
+  number={10},
+  pages={P10008},
+  year={2008},
+  publisher={IOP Publishing}
+}
+
+@article{kaminker2002transposable,
+  title={The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective},
+  author={Kaminker, Joshua S and Bergman, Casey M and Kronmiller, Brent and Carlson, Joseph and Svirskas, Robert and Patel, Sandeep and Frise, Erwin and Wheeler, David A and Lewis, Suzanna E and Rubin, Gerald M and others},
+  journal={Genome biology},
+  volume={3},
+  number={12},
+  pages={research0084--1},
+  year={2002},
+  publisher={BioMed Central}
+}
+
+@article{koren2012hybrid,
+  title={Hybrid error correction and de novo assembly of single-molecule sequencing reads},
+  author={Koren, Sergey and Schatz, Michael C and Walenz, Brian P and Martin, Jeffrey and Howard, Jason T and Ganapathy, Ganeshkumar and Wang, Zhong and Rasko, David A and McCombie, W Richard and Jarvis, Erich D and others},
+  journal={Nature biotechnology},
+  volume={30},
+  number={7},
+  pages={693},
+  year={2012},
+  publisher={Nature Publishing Group}
+}
+
+@article{she2004structure,
+  title={The structure and evolution of centromeric transition regions within the human genome},
+  author={She, Xinwei and Horvath, Julie E and Jiang, Zhaoshi and Liu, Ge and Furey, Terrence S and Christ, Laurie and Clark, Royden and Graves, Tina and Gulden, Cassy L and Alkan, Can and others},
+  journal={Nature},
+  volume={430},
+  number={7002},
+  pages={857},
+  year={2004},
+  publisher={Nature Publishing Group}
+}
+
+@article{skaletsky2003male,
+  title={The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes},
+  author={Skaletsky, Helen and Kuroda-Kawaguchi, Tomoko and Minx, Patrick J and Cordum, Holland S and Hillier, LaDeana and Brown, Laura G and Repping, Sjoerd and Pyntikova, Tatyana and Ali, Johar and Bieri, Tamberlyn and others},
+  journal={Nature},
+  volume={423},
+  number={6942},
+  pages={825},
+  year={2003},
+  publisher={Nature Publishing Group}
+}
+
+@article{riethman2004mapping,
+  title={Mapping and initial analysis of human subtelomeric sequence assemblies},
+  author={Riethman, Harold and Ambrosini, Anthony and Castaneda, Carlos and Finklestein, Jeffrey and Hu, Xue-Lan and Mudunuri, Uma and Paul, Sheila and Wei, Jun},
+  journal={Genome research},
+  volume={14},
+  number={1},
+  pages={18--28},
+  year={2004},
+  publisher={Cold Spring Harbor Lab}
+}
+
+@article{alkan2007organization,
+  title={Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data},
+  author={Alkan, Can and Ventura, Mario and Archidiacono, Nicoletta and Rocchi, Mariano and Sahinalp, S Cenk and Eichler, Evan E},
+  journal={PLoS computational biology},
+  volume={3},
+  number={9},
+  pages={e181},
+  year={2007},
+  publisher={Public Library of Science}
+}
+
+@article{rudd2004analysis,
+  title={Analysis of the centromeric regions of the human genome assembly},
+  author={Rudd, M Katharine and Willard, Huntington F},
+  journal={Trends in genetics},
+  volume={20},
+  number={11},
+  pages={529--533},
+  year={2004},
+  publisher={Elsevier}
+}
+
+@article{myers2000whole,
+  title={A whole-genome assembly of Drosophila},
+  author={Myers, Eugene W and Sutton, Granger G and Delcher, Art L and Dew, Ian M and Fasulo, Dan P and Flanigan, Michael J and Kravitz, Saul A and Mobarry, Clark M and Reinert, Knut HJ and Remington, Karin A and others},
+  journal={Science},
+  volume={287},
+  number={5461},
+  pages={2196--2204},
+  year={2000},
+  publisher={American Association for the Advancement of Science}
+}
+
+@book{peterson2013plant,
+  title={Plant transposable elements: methods and protocols},
+  author={Peterson, Thomas Allen and Peterson, Thomas Allen},
+  year={2013},
+  publisher={Springer}
+}
+
+@article{ummat2014resolving,
+  title={Resolving complex tandem repeats with long reads},
+  author={Ummat, Ajay and Bashir, Ali},
+  journal={Bioinformatics},
+  volume={30},
+  number={24},
+  pages={3491--3498},
+  year={2014},
+  publisher={Oxford University Press}
+}
+
+@article{horvath2000mosaic,
+  title={The mosaic structure of human pericentromeric DNA: a strategy for characterizing complex regions of the human genome},
+  author={Horvath, Juliann E and Schwartz, Stuart and Eichler, Evan E},
+  journal={Genome research},
+  volume={10},
+  number={6},
+  pages={839--852},
+  year={2000},
+  publisher={Cold Spring Harbor Lab}
+}
+
+@article{han2010mite,
+  title={MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences},
+  author={Han, Yujun and Wessler, Susan R},
+  journal={Nucleic acids research},
+  volume={38},
+  number={22},
+  pages={e199--e199},
+  year={2010},
+  publisher={Oxford University Press}
+}
+
+@article{shen2009detect,
+  title={Detect overlapping and hierarchical community structure in networks},
+  author={Shen, Huawei and Cheng, Xueqi and Cai, Kai and Hu, Mao-Bin},
+  journal={Physica A: Statistical Mechanics and its Applications},
+  volume={388},
+  number={8},
+  pages={1706--1712},
+  year={2009},
+  publisher={Elsevier}
+}
+
+@article{palla2005uncovering,
+  title={Uncovering the overlapping community structure of complex networks in nature and society},
+  author={Palla, Gergely and Der{\'e}nyi, Imre and Farkas, Ill{\'e}s and Vicsek, Tam{\'a}s},
+  journal={Nature},
+  volume={435},
+  number={7043},
+  pages={814},
+  year={2005},
+  publisher={Nature Publishing Group}
+}
+
+@article{xie2013overlapping,
+  title={Overlapping community detection in networks: The state-of-the-art and comparative study},
+  author={Xie, Jierui and Kelley, Stephen and Szymanski, Boleslaw K},
+  journal={Acm computing surveys (csur)},
+  volume={45},
+  number={4},
+  pages={43},
+  year={2013},
+  publisher={ACM}
+}
+
+@article{kannan2004clusterings,
+  title={On clusterings: Good, bad and spectral},
+  author={Kannan, Ravi and Vempala, Santosh and Vetta, Adrian},
+  journal={Journal of the ACM (JACM)},
+  volume={51},
+  number={3},
+  pages={497--515},
+  year={2004},
+  publisher={ACM}
+}
+
+@article{brandes2007engineering,
+  title={Engineering graph clustering: Models and experimental evaluation},
+  author={Brandes, Ulrik and Gaertler, Marco and Wagner, Dorothea},
+  journal={ACM Journal of Experimental Algorithmics},
+  volume={12},
+  number={1.1},
+  pages={1--26},
+  year={2007}
+}
+
+@article{tomita2006worst,
+  title={The worst-case time complexity for generating all maximal cliques and computational experiments},
+  author={Tomita, Etsuji and Tanaka, Akira and Takahashi, Haruhisa},
+  journal={Theoretical Computer Science},
+  volume={363},
+  number={1},
+  pages={28--42},
+  year={2006},
+  publisher={Elsevier}
+}
+
+@inproceedings{zhang2005genome,
+  title={Genome-scale computational approaches to memory-intensive applications in systems biology},
+  author={Zhang, Yun and Abu-Khzam, Faisal N and Baldwin, Nicole E and Chesler, Elissa J and Langston, Michael A and Samatova, Nagiza F},
+  booktitle={Supercomputing, 2005. Proceedings of the ACM/IEEE SC 2005 Conference},
+  pages={12--12},
+  year={2005},
+  organization={IEEE}
+}
+
+@article{brandes2001faster,
+  title={A faster algorithm for betweenness centrality},
+  author={Brandes, Ulrik},
+  journal={Journal of mathematical sociology},
+  volume={25},
+  number={2},
+  pages={163--177},
+  year={2001},
+  publisher={Taylor \& Francis}
+}
+
+@article{guy2000genomic,
+  title={Genomic sequence and transcriptional profile of the boundary between pericentromeric satellites and genes on human chromosome arm 10q},
+  author={Guy, J and Spalluto, C and McMurray, A and Hearn, T and Crosier, M and Viggiano, L and Miolla, V and Archidiacono, N and Rocchi, M and Scott, C and others},
+  journal={Human molecular genetics},
+  volume={9},
+  number={13},
+  pages={2029--2042},
+  year={2000},
+  publisher={Oxford University Press}
+}

build.sh

@@ -0,0 +1,26 @@
+#!/bin/sh
+#
+# Compiles the project
+#
+SOURCE_DIR="./src"
+SOURCE_DIR_NESTED="${SOURCE_DIR}/de/mpi_cbg/revant"
+BUILD_DIR="./bin"
+DEBUGGING_INFO="1"  # 0/1
+
+
+COMPILER_FLAGS="-deprecation"    # "-deprecation -Xlint"
+if [ ${DEBUGGING_INFO} -eq 0 ]; then
+	COMPILER_FLAGS="${COMPILER_FLAGS} -g:none"
+fi
+if [ ! -e ${BUILD_DIR} ]; then
+	mkdir ${BUILD_DIR}
+fi
+rm -rf ${BUILD_DIR}
+mkdir ${BUILD_DIR}
+javac ${COMPILER_FLAGS} -d ${BUILD_DIR} ${SOURCE_DIR_NESTED}/util/*.java
+javac ${COMPILER_FLAGS} -cp ${BUILD_DIR} -d ${BUILD_DIR} ${SOURCE_DIR_NESTED}/factorize/*.java
+javac ${COMPILER_FLAGS} -cp ${BUILD_DIR} -d ${BUILD_DIR} ${SOURCE_DIR_NESTED}/intervalgraph/*.java
+javac ${COMPILER_FLAGS} -cp ${BUILD_DIR} -d ${BUILD_DIR} ${SOURCE_DIR_NESTED}/fragments/*.java
+javac ${COMPILER_FLAGS} -cp ${BUILD_DIR} -d ${BUILD_DIR} ${SOURCE_DIR_NESTED}/consensus/*.java
+javac ${COMPILER_FLAGS} -cp ${BUILD_DIR} -d ${BUILD_DIR} ${SOURCE_DIR_NESTED}/graphics/*.java
+javac ${COMPILER_FLAGS} -cp ${BUILD_DIR} -d ${BUILD_DIR} ${SOURCE_DIR_NESTED}/biology/*.java

buildDoc.sh

@@ -0,0 +1,14 @@
+#!/bin/sh
+#
+# Builds the documentation of the project.
+#
+SOURCE_DIR="./src"
+DOCS_DIR="./docs"
+
+
+if [ ! -e ${DOCS_DIR} ]; then
+	mkdir ${DOCS_DIR}
+fi
+javadoc -quiet -sourcepath ${SOURCE_DIR} -d ${DOCS_DIR} de.mpi_cbg.revant.util de.mpi_cbg.revant.factorize de.mpi_cbg.revant.intervalgraph \
+												 	    de.mpi_cbg.revant.fragments de.mpi_cbg.revant.consensus de.mpi_cbg.revant.graphics \
+												 		de.mpi_cbg.revant.biology